Nucleic acid and corresponding protein entitled 161P2F10B useful in treatment and detection of cancer

ABSTRACT

A novel gene 0161P2F10B (also designated 161P2F10B) and its encoded protein, and variants thereof, are described wherein 161P2F10B exhibits tissue specific expression in normal adult tissue, and is aberranty expressed in the cancers listed in Table I. Consequently, 161P2F10B provides a diagnostic, prognostic, prophylactic and/or therapeutic target for cancer. The 161P2F10B gene or fragment thereof, or its encoded protein, or variants thereof, or a fragment thereof, can be used to elicit a humoral or cellular immune response; antibodies or T cells reactive with 161P2F10B can be used in active or passive immunization.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority from U.S. patent application Ser. No. 10/005,480, filed Nov. 7, 2001 (now abandoned); and U.S. patent application Ser. No. 10/062,109, filed Jan. 31, 2002. The contents of each application listed in this paragraph are fully incorporated by reference herein for all purposes.

STATEMENT OF RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH

Not applicable.

FIELD OF THE INVENTION

The invention described herein relates to a gene and its encoded protein, termed 161P2F10B, expressed in certain cancers, and to diagnostic and therapeutic methods and compositions useful in the management of cancers that express 161P2F10B.

BACKGROUND OF THE INVENTION

Cancer is the second leading cause of human death next to coronary disease. Worldwide, millions of people die from cancer every year. In the United States alone, as reported by the American Cancer Society, cancer causes the death of well over a half-million people annually, with over 1.2 million new cases diagnosed per year. While deaths from heart disease have been declining significantly, those resulting from cancer generally are on the rise. In the early part of the next century, cancer is predicted to become the leading cause of death.

Worldwide, several cancers stand out as the leading killers. In particular, carcinomas of the lung, prostate, breast, colon, pancreas, and ovary represent the primary causes of cancer death. These and virtually all other carcinomas share a common lethal feature. With very few exceptions, metastatic disease from a carcinoma is fatal. Moreover, even for those cancer patients who initially survive their primary cancers, common experience has shown that their lives are dramatically altered. Many cancer patients experience strong anxieties driven by the awareness of the potential for recurrence or treatment failure. Many cancer patients experience physical debilitations following treatment. Furthermore, many cancer patients experience a recurrence.

Worldwide, prostate cancer is the fourth most prevalent cancer in men. In North America and Northern Europe, it is by far the most common cancer in males and is the second leading cause of cancer death in men. In the United States alone, well over 30,000 men die annually of this disease—second only to lung cancer. Despite the magnitude of these figures, there is still no effective treatment for metastatic prostate cancer. Surgical prostatectomy, radiation therapy, hormone ablation therapy, surgical castration and chemotherapy continue to be the main treatment modalities. Unfortunately, these treatments are ineffective for many and are often associated with undesirable consequences.

On the diagnostic front, the lack of a prostate tumor marker that can accurately detect early-stage, localized tumors remains a significant limitation in the diagnosis and management of this disease. Although the serum prostate specific antigen (PSA) assay has been a very useful tool, however its specificity and general utility is widely regarded as lacking in several important respects.

Progress in identifying additional specific markers for prostate cancer has been improved by the generation of prostate cancer xenografts that can recapitulate different stages of the disease in mice. The LAPC (Los Angeles Prostate Cancer) xenografts are prostate cancer xenografts that have survived passage in severe combined immune deficient (SCID) mice and have exhibited the capacity to mimic the transition from androgen dependence to androgen independence (Klein et al., 1997, Nat. Med. 3:402). More recently identified prostate cancer markers include PCTA-1 (Su et al., 1996, Proc. Natl. Acad. Sci. USA 93: 7252), prostate-specific membrane (PSM) antigen (Pinto et al., Clin Cancer Res 1996 Sep 2 (9): 1445–51), STEAP (Hubert, et al., Proc Natl Acad Sci USA. Dec. 7, 1999; 96(25): 14523–8) and prostate stem cell antigen (PSCA) (Reiter et a., 1998, Proc. Natl. Acad. Sci. USA 95: 1735).

While previously identified markers such as PSA, PSM, PCTA and PSCA have facilitated efforts to diagnose and treat prostate cancer, there is need for the identification of additional markers and therapeutic targets for prostate and related cancers in order to further improve diagnosis and therapy.

Renal cell carcinoma (RCC) accounts for approximately 3 percent of adult malignancies. Once adenomas reach a diameter of 2 to 3 cm, malignant potential exists. In the adult, the two principal malignant renal tumors are renal cell adenocarcinoma and transitional cell carcinoma of the renal pelvis or ureter. The incidence of renal cell adenocarcinoma is estimated at more than 29,000 cases in the United States, and more than 11,600 patients died of this disease in 1998. Transitional cell carcinoma is less frequent, with an incidence of approximately 500 cases per year in the United States.

Surgery has been the primary therapy for renal cell adenocarcinoma for many decades. Until recently, metastatic disease has been refractory to any systemic therapy. With recent developments in systemic therapies, particularly, immunotherapies, metastatic renal cell carcinoma may be approached aggressively in appropriate patients with a possibility of durable responses. Nevertheless, there is a remaining need for effective therapies for these patients.

Of all new cases of cancer in the United States, bladder cancer represents approximately 5 percent in men (fifth most common neoplasm) and 3 percent in women (eighth most common neoplasm). The incidence is increasing slowly, concurrent with an increasing older population. In 1998, there was an estimated 54,500 cases, including 39,500 in men and 15,000 in women. The age-adjusted incidence in the United States is 32 per 100,000 for men and eight per 100,000 in women. The historic male/female ratio of 3:1 may be decreasing related to smoking patterns in women. There were an estimated 11,000 deaths from bladder cancer in 1998 (7,800 in men and 3,900 in women). Bladder cancer incidence and mortality strongly increase with age and will be an increasing problem as the population becomes more elderly.

Most bladder cancers recur in the bladder. Bladder cancer is managed with a combination of transurethral resection of the bladder (TUR) and intravesical chemotherapy or immunotherapy. The multifocal and recurrent nature of bladder cancer points out the limitations of TUR. Most muscle-invasive cancers are not cured by TUR alone. Radical cystectomy and urinary diversion is the most effective means to eliminate the cancer but carry an undeniable impact on urinary and sexual function. There continues to be a significant need for treatment modalities that are beneficial for bladder cancer patients.

An estimated 130,200 cases of colorectal cancer occurred in 2000 in the United States, including 93,800 cases of colon cancer and 36,400 of rectal cancer. Colorectal cancers are the third most common cancers in men and women. Incidence rates declined significantly during 1992–1996 (−2.1% per year). Research suggests that these declines have been due to increased screening and polyp removal, preventing progression of polyps to invasive cancers. There were an estimated 56,300 deaths (47,700 from colon cancer, 8,600 from rectal cancer) in 2000, accounting for about 11% of all U.S. cancer deaths.

At present, surgery is the most common form of therapy for colorectal cancer, and for cancers that have not spread, it is frequently curative. Chemotherapy, or chemotherapy plus radiation, is given before or after surgery to most patients whose cancer has deeply perforated the bowel wall or has spread to the lymph nodes. A permanent colostomy (creation of an abdominal opening for elimination of body wastes) is occasionally needed for colon cancer and is infrequently required for rectal cancer. There continues to be a need for effective diagnostic and treatment modalities for colorectal cancer.

There were an estimated 164,100 new cases of lung and bronchial cancer in 2000, accounting for 14% of all U.S. cancer diagnoses. The incidence rate of lung and bronchial cancer is declining significantly in men, from a high of 86.5 per 100,000 in 1984 to 70.0 in 1996 In the 1990s, the rate of increase among women began to slow. In 1996, the incidence rate in women was 42.3 per 100,000.

Lung and bronchial cancer caused an estimated 156,900 deaths in 2000, accounting for 28% of all cancer deaths. During 1992–1996, mortality from lung cancer declined significantly among men (−1.7% per year) while rates for women were still significantly increasing (0.9% per year). Since 1987, more women have died each year of lung cancer than breast cancer, which, for over 40 years, was the major cause of cancer death in women. Decreasing lung cancer incidence and mortality rates most likely resulted from decreased smoking rates over the previous 30 years; however, decreasing smoking patterns among women lag behind those of men. Of concern, although the declines in adult tobacco use have slowed, tobacco use in youth is increasing again.

Treatment options for lung and bronchial cancer are determined by the type and stage of the cancer and include surgery, radiation therapy, and chemotherapy. For many localized cancers, surgery is usually the treatment of choice. Because the disease has usually spread by the time it is discovered, radiation therapy and chemotherapy are often needed in combination with surgery. Chemotherapy alone or combined with radiation is the treatment of choice for small cell lung cancer; on this regimen, a large percentage of patients experience remission, which in some cases is long lasting. There is however, an ongoing need for effective treatment and diagnostic approaches for lung and bronchial cancers.

An estimated 182,800 new invasive cases of breast cancer were expected to occur among women in the United States during 2000. Additionally, about 1,400 new cases of breast cancer were expected to be diagnosed in men in 2000. After increasing about 4% per year in the 1980s, breast cancer incidence rates in women have leveled off in the 1990s to about 110.6 cases per 100,000.

In the U.S. alone, there were an estimated 41,200 deaths (40,800 women, 400 men) in 2000 due to breast cancer. Breast cancer ranks second among cancer deaths in women. According to the most recent data, mortality rates declined significantly during 1992–1996 with the largest decreases in younger women, both white and black. These decreases were probably the result of earlier detection and improved treatment.

Taking into account the medical circumstances and the patient's preferences, treatment of breast cancer may involve lumpectomy (local removal of the tumor) and removal of the lymph nodes under the arm; mastectomy (surgical removal of the breast) and removal of the lymph nodes under the arm; radiation therapy; chemotherapy; or hormone therapy. Often, two or more methods are used in combination. Numerous studies have shown that, for early stage disease, long-term survival rates after lumpectomy plus radiotherapy are similar to survival rates after modified radical mastectomy. Significant advances in reconstruction techniques provide several options for breast reconstruction after mastectomy. Recently, such reconstruction has been done at the same time as the mastectomy.

Local excision of ductal carcinoma in situ (DCIS) with adequate amounts of surrounding normal breast tissue may prevent the local recurrence of the DCIS. Radiation to the breast and/or tamoxifen may reduce the chance of DCIS occurring in the remaining breast tissue. This is important because DCIS, if left untreated, may develop into invasive breast cancer. Nevertheless, there are serious side effects or sequelae to these treatments. There is, therefore, a need for efficacious breast cancer treatments.

There were an estimated 23,100 new cases of ovarian cancer in the United States in 2000. It accounts for 4% of all cancers among women and ranks second among gynecologic cancers. During 1992–1996, ovarian cancer incidence rates were significantly declining. Consequent to ovarian cancer, there were an estimated 14,000 deaths in 2000. Ovarian cancer causes more deaths than any other cancer of the female reproductive system.

Surgery, radiation therapy, and chemotherapy are treatment options for ovarian cancer. Surgery usually includes the removal of one or both ovaries, the fallopian tubes (salpingo-oophorectomy), and the uterus (hysterectomy). In some very early tumors, only the involved ovary will be removed, especially in young women who wish to have children. In advanced disease, an attempt is made to remove all intra-abdominal disease to enhance the effect of chemotherapy. There continues to be an important need for effective treatment options for ovarian cancer.

There were an estimated 28,300 new cases of pancreatic cancer in the United States in 2000. Over the past 20 years, rates of pancreatic cancer have declined in men. Rates among women have remained approximately constant but may be beginning to decline. Pancreatic cancer caused an estimated 28,200 deaths in 2000 in the United States. Over the past 20 years, there has been a slight but significant decrease in mortality rates among men (about −0.9% per year) while rates have increased slightly among women.

Surgery, radiation therapy, and chemotherapy are treatment options for pancreatic cancer. These treatment options can extend survival and/or relieve symptoms in many patients but are not likely to produce a cure for most. There is a significant need for additional therapeutic and diagnostic options for pancreatic cancer.

SUMMARY OF THE INVENTION

The present invention relates to a gene, designated 161P2F10B, that has now been found to be over-expressed in the cancer(s) listed in Table I. Northern blot expression analysis of 161P2F10B gene expression in normal tissues shows a restricted expression pattern in adult tissues. The nucleotide (FIG. 2) and amino acid (FIG. 2, and FIG. 3) sequences of 161P2F10B are provided. The tissue-related profile of 161P2F10B in normal adult tissues, combined with the over-expression observed in the tissues listed in Table I, shows that 161P2F10B is aberrantly over-expressed in at least some cancers, and thus serves as a useful diagnostic, prophylactic, prognostic, and/or therapeutic target for cancers of the tissue(s) such as those listed in Table I.

The invention provides polynucleotides corresponding or complementary to all or part of the 161P2F10B genes, mRNAs, and/or coding sequences, preferably in isolated form, including polynucleotides encoding 161P2F10B-related proteins and fragments of 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more than 25 contiguous amino acids; at least 30, 35, 40, 45, 50, 55, 60, 65, 70, 80, 85, 90, 95, 100 or more than 100 contiguous amino acids of a 161P2F10B-related protein, as well as the peptides/proteins themselves; DNA, RNA, DNA/RNA hybrids, and related molecules, polynucleotides or oligonucleotides complementary or having at least a 90% homology to the 161P2F10B genes or mRNA sequences or parts thereof, and polynucleotides or oligonucleotides that hybridize to the 161P2F10B genes, mRNAs, or to 161P2F10B-encoding polynucleotides. Also provided are means for isolating cDNAs and the genes encoding 161P2F10B. Recombinant DNA molecules containing 161P2F10B polynucleotides, cells transformed or transduced with such molecules, and host-vector systems for the expression of 161P2F10B gene products are also provided. The invention further provides antibodies that bind to 161P2F10B proteins and polypeptide fragments thereof, including polyclonal and monoclonal antibodies, murine and other mammalian antibodies, chimeric antibodies, humanized and fully human antibodies, and antibodies labeled with a detectable marker or therapeutic agent. In certain embodiments, there is a proviso that the entire nucleic acid sequence of FIG. 2 is not encoded and/or the entire amino acid sequence of FIG. 2 is not prepared. In certain embodiments, the entire nucleic acid sequence of FIG. 2 is encoded and/or the entire amino acid sequence of FIG. 2 is prepared, either of which are in respective human unit dose forms.

The invention further provides methods for detecting the presence and status of 161P2F10B polynucleotides and proteins in various biological samples, as well as methods for identifying cells that express 161P2F10B. A typical embodiment of this invention provides methods for monitoring 161P2F10B gene products in a tissue or hematology sample having or suspected of having some form of growth dysregulation such as cancer.

The invention further provides various immunogenic or therapeutic compositions and strategies for treating cancers that express 161P2F10B such as cancers of tissues listed in Table I, including therapies aimed at inhibiting the transcription, translation, processing or function of 161P2F10B as well as cancer vaccines. In one aspect, the invention provides compositions, and methods comprising them, for treating a cancer that expresses 161P2F10B in a human subject wherein the composition comprises a carrier suitable for human use and a human unit dose of one or more than one agent that inhibits the production or function of 161P2F10B. Preferably, the carrier is a uniquely human carrier. In another aspect of the invention, the agent is a moiety that is immunoreactive with 161P2F10B protein. Non-limiting examples of such moieties include, but are not limited to, antibodies (such as single chain, monoclonal, polyclonal, humanized, chimeric, or human antibodies), functional equivalents thereof (whether naturally occurring or synthetic), and combinations thereof. The antibodies can be conjugated to a diagnostic or therapeutic moiety. In another aspect, the agent is a small molecule as defined herein.

In another aspect, the agent comprises one or more than one peptide which comprises a cytotoxic T lymphocyte (CTL) epitope that binds an HLA class I molecule in a human to elicit a CTL response to 161P2F10B and/or one or more than one peptide which comprises a helper T lymphocyte (HTL) epitope which binds an HLA class II molecule in a human to elicit an HTL response. The peptides of the invention may be on the same or on one or more separate polypeptide molecules. In a further aspect of the invention, the agent comprises one or more than one nucleic acid molecule that expresses one or more than one of the CTL or HTL response stimulating peptides as described above. In yet another aspect of the invention, the one or more than one nucleic acid molecule may express a moiety that is immunologically reactive with 161P2F10B as described above. The one or more than one nucleic acid molecule may also be, or encodes, a molecule that inhibits production of 161P2F10B. Non-limiting examples of such molecules include, but are not limited to, those complementary to a nucleotide sequence essential for production of 161P2F10B (e.g. antisense sequences or molecules that form a triple helix with a nucleotide double helix essential for 161P2F10B production) or a ribozyme effective to lyse 161P2F10B mRNA.

Note that to determine the starting position of any peptide set forth in Tables VIII–XXI and XXII to XLIX (collectively HLA Peptide Tables) respective to its parental protein, e.g., variant 1, variant 2, etc., reference is made to three factors: the particular variant, the length of the peptide in an HLA Peptide Table, and the Search Peptides in Table VII. Generally, a unique Search Peptide is used to obtain HLA peptides of a particular for a particular variant. The position of each Search Peptide relative to its respective parent molecule is listed in Table VII. Accordingly, if a Search Peptide begins at position “X”, one must add the value “X−1” to each position in Tables VIII–XXI and XXII to XLIX to obtain the actual position of the HLA peptides in their parental molecule. For example, if a particular Search Peptide begins at position 150 of its parental molecule, one must add 150-1, i.e., 149 to each HLA peptide amino acid position to calculate the position of that amino acid in the parent molecule.

One embodiment of the invention comprises an HLA peptide, that occurs at least twice in Tables VIII–XXI and XXII to XLIX collectively, or an oligonucleotide that encodes the HLA peptide. Another embodiment of the invention comprises an HLA peptide that occurs at least once in Tables VIII-XXI and at least once in tables XXII to XLIX, or an oligonucleotide that encodes the HLA peptide.

Another embodiment of the invention is antibody epitopes, which comprise a peptide regions, or an oligonucleotide encoding the peptide region, that has one two, three, four, or five of the following characteristics:

i) a peptide region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Hydrophilicity profile of FIG. 5;

ii) a peptide region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or less than 0.5, 0.4, 0.3, 0.2, 0.1, or having a value equal to 0.0, in the Hydropathicity profile of FIG. 6;

iii) a peptide region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Percent Accessible Residues profile of FIG. 7;

iv) a peptide region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Average Flexibility profile of FIG. 8; or

v) a peptide region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Beta-turn profile of FIG. 9.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1. The 161P2F10B SSH sequence of 182 nucleotides.

FIG. 2. A) The cDNA and amino acid sequence of 161P2F10B variant 1 (also called “161P2F10B v 1” or “161P2F10B variant 1”) is shown in FIG. 2A. The start methionine is underlined. The open reading frame extends from nucleic acid 44-2671 including the stop codon.

B) The cDNA and amino acid sequence of 161P2F10B variant 2 (also called “161P2F10B v.2”) is shown in FIG. 2B. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 44-2671 including the stop codon.

C) The cDNA and amino acid sequence of 161P2F10B variant 3 (also called “161P2F10B v.3”) is shown in FIG. 2C. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 44-2671 including the stop codon. The cDNA and amino acid sequence of 161P2F10B variant4 (also called “161P2F10B v.4”) is shown in

D) FIG. 2D. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 44-2671 including the stop codon.

E) The cDNA and amino acid sequence of 161P2F10B variant 5 (also called “161P2F10B v.5”) is shown in FIG. 2E. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 44-2671 including the stop codon.

F) The cDNA and amino acid sequence of 161P2F10B variant 6 (also called “161P2F10B v.6”) is shown in FIG. 2F. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 84–2711 including the stop codon.

G) The cDNA and amino acid sequence of 161P2F10B variant 7 (also called “161P2F10B v.7”) is shown in FIG. 2G. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 276-2801 including the stop codon.

FIG. 3.

A) Amino acid sequence of 161P2F10B v.1 is shown in FIG. 3A; it has 875 amino acids.

B) The amino acid sequence of 161P2F10B v.2 is shown in FIG. 3B; it has 875 amino acids.

C) The amino acid sequence of 161P2F10B v.3 is shown in FIG. 3C; it has 875 amino acids.

D) The amino acid sequence of 161P2F10B v.4 is shown in FIG. 3D; it has 875 amino acids.

E) The amino acid sequence of 161P2F10B v.7 is shown in FIG. 3E; it has 841 amino acids. As used herein, a reference to 161P2F-10B includes all variants thereof, including those shown in FIGS. 2, 3, 10, and 11, unless the context clearly indicates otherwise.

FIG. 4. FIG. 4A: Alignment of 161P2F10 with variant 1 carrying a K to R mutation. FIG. 4B: Alignment of 161P2F10B and SNP variant carrying a T to P mutation.

FIG. 5. Hydrophilicity amino acid profile of 161P2F10B determined by computer algorithm sequence analysis using the method of Hopp and Woods (Hopp T. P., Woods K. R., 1981. Proc. Natl. Acad. Sci. U.S.A. 78:3824–3828) accessed on the Protscale website located on the World Wide Web through the ExPasy molecular biology server.

FIG. 6. Hydropathicity amino acid profile of 161P2F10B determined by computer algorithm sequence analysis using the method of Kyte and Doolittle (Kyte J., Doolittle R. F., 1982. J. Mol. Biol. 157:105–132) accessed on the ProtScale website located on the World Wide Web through the ExPasy molecular biology server.

FIG. 7. Percent accessible residues amino acid profile of 161P2F10B determined by computer algorithm sequence analysis using the method of Janin (Janin J., 1979 Nature 277:49 1–492) accessed on the ProtScale website located on the World Wide Web through the ExPasy molecular biology server.

FIG. 8. Average flexibility amino acid profile of 161P2F10B determined by computer algorithm sequence analysis using the method of Bhaskaran and Ponnuswamy (Bhaskaran R., and Ponnuswamy P. K., 1988. Int. J. Pept. Protein Res. 32:242–255) accessed on the ProtScale website located on the World Wide Web through the ExPasy molecular biology server.

FIG. 9. Beta-turn amino acid profile of 161P2F10B determined by computer algorithm sequence analysis using the method of Deleage and Roux (Deleage, G., Roux B. 1987 Protein Engineering 1:289–294) accessed on the ProtScale website located on the World Wide Web through the ExPasy molecular biology server.

FIG. 10. Variants 161P2F10B v.2 through v.5 are variants with single nucleotide differences. Though these SNP variants are shown separately, they could also occur in any combinations and in any transcript variants that contains the base pairs. Variants 161P2F10B v.6 and v.7 are transcript variants. Variant 161P2F10B v.6 has extra 40 bases at the 5′ end and a different 3′ end portion, while variant 161P2F10B v.7 has an insertion of 130 bases in between positions 121 and 122 of 161P2F10B v.1. Numbers in “( )” correspond to those of 161P2F10B v.1. Black box shows the same sequence as 161P2F10B v.1. SNPs are indicated above the box.

FIG. 11. Protein variants correspond to nucleotide variants. Nucleotide variants 161P2F10B v.5 and v.6 in FIG. 10 code for the same protein as 161P2F10B v.1. Nucleotide variants 161P2F10B v.6 and v.7 are splice variants of v.1, as shown in FIG. 12. Single amino acid differences were indicated above the boxes. Black boxes represent the same sequence as 161 P2F10B v.1. Numbers underneath the box correspond to 161 P2F10B v.1.

FIG. 12. Intentionally Omitted

FIG. 13. The secondary structure of 161P2F10B (SEQ ID NO: 103), namely the predicted presence and location of alpha helices, extended strands, and random coils, is predicted from the primary amino acid sequence using the HNN—Hierarchical Neural Network method, accessed from the ExPasy molecular biology server. The analysis indicates that 161P2F10B is composed 31.31% alpha helix, 11.31% extended strand, and 57.37% random coil (FIG. 13A). Shown graphically in FIG. 13 panels B and C are the results of analysis using the TMpred (FIG. 13B) and TMHMM (FIG. 13C) prediction programs depicting the location of the transmembrane domain.

FIG. 14. First strand cDNA was generated from normal stomach, normal brain, normal heart, normal liver, normal skeletal muscle, normal testis, normal prostate, normal bladder, normal kidney, normal colon, normal lung, normal pancreas, and a pool of cancer specimens from prostate cancer patients, bladder cancer patients, kidney cancer patients, colon cancer patients, lung cancer patients, pancreas cancer patients, a pool of prostate cancer xenografts (LAPC-4AD, LAPC-4AI, LAPC-9AD and LAPC-9AI), and a pool of 2 patient prostate metastasis to lymph node. Normalization was performed by PCR using primers to actin. Semi-quantitative PCR, using primers to 161P2F10B, was performed at 26 and 30 cycles of amplification. Samples were run on an agarose gel, and PCR products were quantitated using the Alphalmager software. Results show strong expression in prostate cancer, bladder cancer, kidney cancer, colon cancer, lung cancer, pancreas cancer, bone cancer, lymphoma cancer, uterus cancer, compared to all normal tissues tested. Strong expression was also detected in the xenograft pool as well as the prostate cancer metastasis to lymph node specimens.

FIG. 15. First strand cDNA was prepared from a panel of kidney cancer clear cell carcinoma (A), kidney cancer papillary carcinoma (B), and in uterus patient cancer specimens (C). Normalization was performed by PCR using primers to actin. Semi-quantitative PCR, using primers to 161P2F10B, was performed at 26 and 30 cycles of amplification. Samples were run on an agarose gel, and PCR products were quantitated using the Alphalmager software. Expression was recorded as absent, low, medium or strong. Results show expression of 161P2F10B in 94.7% of clear cell renal carcinoma, 62.5% of papillary renal cell carcinoma, and in 61.5% of uterus cancer.

FIG. 16. Shows Phosphodiesterase Activity of 3T3-161P2F10B Stable Cells. Cell surface phosphodiesterase activity is assayed on 3T3 and 3T3-161P2F10B using the substrate p-nitrophenyl thymidine-5′-L-monosphosphate.

FIG. 17. Shows Protection from Apoptosis by 161P2F10B.

FIG. 18. Shows that 161P2F10B Protects from Apoptotic Signals.

FIG. 19. Shows that 161P2F10B Protects from Staurosporine and UV-Induced Apoptosis.

FIG. 20. Shows that 161P2F10B Expression Protects Cells from Drug and UV-Induced Apoptosis. NIH 3T3 cells were treated with the staurosporine or UV, stained with Annexin V-FITC and propidium iodide, and analyzed by FACS.

FIG. 21. Shows that 161P2F10B Protects from Apoptosis by Chemotherapeutic Agents.

FIG. 22 Shows the effect of 161P2F10B on In Vitro Invasion. Invasion was determined by measuring the fluorescence of cells in the lower chamber relative to the fluorescence of the entire cell population.

FIG. 23. Shows that 161P2F10B MAb Attenuates the Growth of Human Kidney Cancer Xenograft in SCID Mice.

FIG. 24. Detection of 161P2F10B protein by immunohistochemistry in kidney cancer patient specimens. Two renal clear cell carcinoma tissue specimens and one renal papillary cell carcinoma were obtained from three different kidney cancer patients. Frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes. The sections were then incubated with mouse monoclonal anti-ENPP3 antibody (Coulter-Immunotech, Marseilles, France) for 3 hours. The slides were washed three times in buffer, and further incubated with DAKO EnVision+™ peroxidase-conjugated goat anti-mouse secondary antibody (DAKO Corporation, Carpenteria, Calif.) for 1 hour. The sections were then washed in buffer, developed using the DAB kit (SIGMA Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy. The results showed strong expression of 161P2F10B in all three renal carcinoma patient tissues (FIG. 24 panels A–C). The expression was detected mostly around the cell membrane in the renal clear cell carcinoma specimens, indicating that 161P2F10B is membrane associated in this kidney cancer, and throughout the cells in the papillary cell carcinoma with an apparent predisposition towards the cell periphery.

FIG. 25. Detection of 161P2F10B protein by immunohistochemistry in a prostate cancer patient specimen. Tissue specimens of prostate adenocarcinoma were obtained from eight different prostate cancer patients. Frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes. The sections were then incubated with mouse monoclonal anti-ENPP3 antibody (Coulter-Immunotech, Marseilles, France) for 3 hours. The slides were washed three times in buffer, and further incubated with DAKO EnVision+™ peroxidase-conjugated goat anti-mouse secondary antibody (DAKO Corporation, Carpenteria, Calif.) for 1 hour. The sections were then washed in buffer, developed using the DAB kit (SIGMA Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy. The results showed expression of 161P2F10B in six of the eight prostate cancer patient tissues, one of which is illustrated in this FIG. 25. 161P2F10B was expressed on the tumor cells with an apparent proclivity towards the luminal cell surface.

FIG. 26. Detection of 161P2F10B protein by immunohistochemistry in a colon cancer patient specimen. Tissue specimens of colon adenocarcinoma were obtained from nine different colon cancer patients Frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes. The sections were then incubated with mouse monoclonal anti-ENPP3 antibody (Coulter-Immunotech, Marseilles, France) for 3 hours. The slides were washed three times in buffer, and further incubated with DAKO EnVision+™ peroxidase-conjugated goat anti-mouse secondary antibody (DAKO Corporation, Carpenteria, Calif.) for 1 hour. The sections were then washed in buffer, developed using the DAB kit (SIGMA Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy. The results showed strong expression of 161P2F10B in two of the nine colon cancer patient tissues, one of which is illustrated in this FIG. 26. 161P2F10B was most strongly expressed on the tumor cells with a luminal cell surface but was also expressed throughout all the tumor tissue.

FIG. 27. Detection by immunohistochemistry of 161P2F10B protein expression in kidney clear cell cancer patient specimens by specific binding of mouse monoclonal antibodies. Renal clear cell carcinoma tissue and its matched normal adjacent were obtained from a kidney cancer patient. Frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes. The sections were then incubated either mouse monoclonal anti-ENPP3 antibody (Coulter-Immunotech, Marseilles, France) for 3 hours (FIG. 27 panels A, D), or mouse monoclonal antibody X41(3)50 (FIG. 27 panels B, E), or mouse monoclonal antibody X41 (3)37 (FIG. 27 panels C, F). The slides were washed three times in buffer and further incubated with DAKO EnVision+™ peroxidase-conjugated goat anti-mouse secondary antibody (DAKO Corporation, Carpenteria, Calif.) for 1 hour. The sections were then washed in buffer, developed using the DAB kit (SIGMA Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy (FIG. 27 panels A–F). The results showed strong expression of 161P2F10B in the renal clear cell carcinoma patient tissue (FIG. 27 panels A–C), but weakly in normal kidney (FIG. 27 panels D–F). The expression was predominantly around the cell periphery indicating that 161P2F10B is membrane associated in kidney cancer tissues. The weak expression detected in normal kidney was localized to the kidney proximal tubules.

FIG. 28. Expression of 161P2F10b in recombinant cell lines.

A.) Rat1, NIH3T3, NSO, and 300.19 cells stably expressing either 16P2F10b or a control vector (neo) were stained with PE-conjugated anti-CD203c MAb and examined by flow cytometry. (Light dotted line: control neo cells. Dark line: 161P2F10 cells)

B.) Rat1, NIH3T3, NSO, 300.19, and UT7 cells were stained with either PE-conjugated anti-CD203c MAb or control IgG1-PE Ab and examined by flow cytometry. (Light dotted line: control MAb. Dark line: 97A6 (CD203c) MAb.) Shown is the mean fluorescence of the staining of the control and 161P2F10b cells and the ratio of the values. This was used to rank the cells for relative expression levels of 161P2F10b.

C.) The relative cell surface phosphodiesterase enzymatic activity of the recombinant cells was measured by the addition of p-nitrophenyl thymidine-5′-L-monophosphate (p-nTMP) phosphodiesterase substrate. There is a correlation between expression levels determined by flow cytometry and surface enzyme activity.

FIG. 29. Surface expression and phosphodiesterase activity of 161P2F10b.

A. 161P2F10b transfected 293T cells were stained with the commercially available (Coulter Immunotech) PE-conjugated anti-CD-203c MAb, a commercially available anti-ENPP3 (161P2F10b) MAb and examined by fluorescent microscopy.

B. 161P2F10b and vector transfected 293T cells were incubated in assay buffer containing the phosphodiesterase-1 colorimetic substrate p-nitrophenyl thymidine-5′-L-monophosphate (p-nTMP) and optical densities (O.D.) were obtained at 405 nm.

FIG. 30. Relative expression and enzymatic activity of 161P2F10b mutants in recombinant Caki kidney cancer cells. Caki kidney cancer cells were infected with retrovirus containing either wildtype 161P2F120b cDNA, or point mutant cDNAs encoding either a threonine to serine mutation (T/S) at amino acid 205, a threonine to alanine mutation (T/A) at amino acid 205, or a aspartic acid to glutamic acid mutation (DIE) at amino acid 80. Stably expressing cell lines were analyzed for 161P2F10b expression by flow cytometry with 97A6 (CD203c) MAb (A) and for enzymatic activity with p-nTMP substrate (B). Mutation of threonine 205 to aspartic acid or alanine abolishes the ability to cleave the substrate, demonstrating that threonine 205 is critical to the enzymatic activity of 161P2F10b.

FIG. 31. Purification of a recombinant protein encoding the extracellular domain (ECD) of 161P2F10b. 293T cells were transfected with a Tag5 secretion expression vector encoding the ECD of 161P2F10b (amino acids 46–875). The recombinant protein was purified from the conditioned media using either metal chelate affinity chromatography (not shown) or with an immunoaffinity column comprised of anti-161P2F10b MAb X41.6 (shown). 2 ul of 2 separate purified lots were analyzed by SDS-PAGE and Coomasie staining. BSA protein was also analyzed as a quantitative standard.

FIG. 32. 161P2F10b enzymatic assays utilizing P-nitrophenyl-thymidine monophosphate (p-nTMP).

A. Schematic of the colorimetric enzyme assay showing enzymatic cleavage of the p-nTMP substrate generating a soluble yellow product.

B. Kinetics and dose response of the enzymatic action of purified Tag5-ECD 161P2F10b protein on p-nTMP (2.5 mM). Optical densities (OD) of reactions were determined at 405 nm.

C. Cell surface enzymatic assay of 161P2F10b-expressing Rat1 cells. The indicated number of Rat1-161P2F10b cells were incubated with p-nTMP substrate and the OD's of the wells were determined.

D. ATP and NAD (not shown) serve as competitive inhibitors 161P2F10b cleavage of p-nTMP. Purified Tag5-ECD protein (20 ng) was incubated with p-nTMP substrate in the absence or presence of the indicated amounts of ATP. The OD's of reactions were obtained at 405 nm.

FIG. 33. Analysis of the internalization of anti-161P2F10b MAb X41.6.

Panel A. Schematic of the protocol. Rat1-161P2F10b cells are incubated with anti-161P2F10b MAb at 4C, washed, and then either kept at 4C and stained with anti-mouse IgG secondary-PE conjugated Ab at 4C (B, total surface staining) or moved to 37C for various times and then stained with secondary Ab at 4C (C, residual surface staining). Panels B and C demonstrate that MAb X41.6 engagement of surface 161P2F10b causes internalization at 37C of the complex indicated by the progressive decrease in mean fluorescence intensity (MFI).

FIG. 34. Internalization of selected anti-161P2F10b murine MAbs. Internalization of selected anti-161P2F10b MAbs are by flow cytometry are shown. Internalization is indicated by a decrease in the mean fluorescence intensity (MFI) of cells moved to 37C versus cells stained at 4C.

FIG. 35. Antibody engagement of 161P2F10b results in its internalization. Internalization of the commercially available MAb 97A6, anti-CD203c, is shown by fluorescence microscopy following staining of Rat1-161P2F10b cells. The cells were incubated with CD203c-PE conjugated MAb at 4C, washed, and then moved to 37C for the indicated times and then examined by fluorescence microscopy. At 4C, the staining of the cells is cell surface (bright halo of fluorescence around individual cells). Upon moving to 37C, there is a gradual loss of the surface fluorescence, concomitant with capping of the MAb to punctate regions on the surface, followed by the appearance of punctate and diffuse intracellular fluorescence and a total loss of surface fluorescence.

FIG. 36. Effects of X41.50 MAb-saporin toxin conjugate on Caki-161P2F10b cells. Shown is the morphology of Caki-161P2F10b cells that were treated with and without the indicated concentrations of the internalizing anti-161P2F10b MAb and an anti-mouse IgG-saporin toxin secondary Ab (2 ug/ml). Saporin is unable to enter cells efficiently on its own and must be internalized for its toxic mechanism (protein synthesis inhibition) to work. Cells were first incubated at 4C with X41.50 MAb to allow surface binding, than either media or the saporin-conjugated secondary Ab was added and the cells were incubated for 72 hours at 37C. Cells incubated with either media alone, X41.50 alone, or the secondary-saponn Ab alone had no effect on Caki-161P2F10b growth and morphology, exemplified by a viable confluent monolayer. However, cells incubated with X41.50 MAb (2 and 0.5 ug/ml) and the secondary saporin-conjugate exhibited signs of growth inhibition (did not reach confluency) and apoptosis (small round floating apoptotic cells above the attached cell layer). This demonstrates the utility of anti-161P2F10b MAbs drug/toxin conjugates as a therapeutic approach for 161P2F10b-expressing cancers and diseased tissues.

FIG. 37. Internalization-mediated downregulation of 161P2F10 protein by MAb X41.50. Rat1-161P2F10b cells were incubated with and without 10 ug/ml of MAb X41.50 for 72 hours. Cells were washed, fixed, permeabilized, and stained with PE-conjugated CD203c MAb to monitor total 161P2F10b protein expression. The data shows a marked decrease in staining following treatment of the cells with X41.50, demonstrating downregulation of 161P2F10b protein.

FIG. 38. Anti-161P2F10b MAbs downregulate surface 161P2F10b enzymatic activity. Rat1-161P2F10b cells were treated with and without various concentrations of the indicated MAbs for 48 hours and then assayed for surface enzymatic activity using p-n-TMB substrate. The data demonstrates that engagement and internalization of surface 161P2F10b by MAbs results in the concamitant loss of surface 161P2F10b enzymatic activity.

FIG. 39. Characteristics of mouse 161P2F10b MAbs. Shown is a summary of various characteristics of MAbs that recognize 161P2F10b.

The relative affinity of the MAbs was determined by saturation binding ELISA using the recombinant Tag5-ECD protein. The Kd of the binding reaction was determined using a one-site binding non-linear regression analysis of the data using GraphPad Prism software version 3.02 (Graphpad Software, San Diego, Calif.).

Relative surface staining was determined using 10 ug/ml of each MAb on RAT1-161P2F10b cells.

Relative ability to internalize was also carried out on Rat1-161P2F10b cells comparing staining with 10 ug/ml of MAb at 4C versus residual staining following incubation at 37C for 30 minutes.

The ability of the MAbs to downregulate surface enzyme activity was determined by incubation of Rat1-161P2F10b cells with 10 ug/ml of each MAb for 72 hours then assaying surface enzyme activity with p-nTMP substrate.

Relative specific immunohistochemical staining (1HC) was determined using 10 ug/ml of each MAb on 161P2F10b-expressing frozen section kidney clear cell carcinoma samples.

The epitope family was determined by competition binding ELISA using the Tag5-ECD protein as target. Tag5-ECD ELISA coated wells were first incubated with or without 10 ug/ml of competitor MAb, washed, and then incubated with 1 ug/ml of HRP-labeled test MAb. MAb that compete for binding (reduction of the signal of the test MAb with prior incubation with competitor) must share the same or an overlapping epitope and are thus assigned to an epitope family. Of the MAbs listed, at least 2 epitope families are defined.

FIG. 40. Surface staining of selected anti-161P2F10b MAbs. Specific binding of cell surface 161P2F10b was determined by incubation of Rat1-161P2F10 (dark line) and Rat1-neo control cells (light dotted line) with 10 ug/ml of each MAb for 1.5 hours at 4C₁-Cells-were washed, incubated with goat-anti-mouse-PE conjugated secondary Ab, washed again, and analyzed by flow cytometry. Shown are examples of MAb derived from DNA-based immunization of mice with an FC-fusion of the ECD (X41.6, X41.15, X41.17, X41.29, X41.37, X41.50), also DNA-based immunization with Tag5-ECD, and with Rat1-161P2F10b cells (the last data was generated using the respective hybridoma supernatant at a 1:50 dilution) was performed.

FIG. 41. Anti-161P2F10b MAbs X41.6 and 97A6 (CD203c) do not cross-react with ENPP1. Conditioned media from 293T cells transfected with either Tag5–161P2F10b or ENPP1 His-tagged vectors was subjected to immunoprecipitation analysis using 5 ug of MAb X41.6, MAb 97A6 (CD203c), or anti-His pAb. Following washing of the immune complexes, phosphodiesterase activity was determined by the addition of p-nTMP substrate. Enzymatic activity is seen in anti-His immune complexes from both Tag5 161P2F10b and Tag5 ENPP1 media due to the presence of the His epitope in both proteins. However, enzymatic activity is seen only in the immune complexes of X41.6 and 97A6 from Tag5 161P2F10 conditioned media and not with Tag5 ENPP1 media. These data demonstrate that MAbs X41.6 and 97A6 (CD203c) do not crossreact with the homologous ectonucleotide pyrophosphatase/phosphodiesterase family member ENPP1.

FIG. 42. Detection of 161P2F10b in the conditioned media of 161P2F10b-expressing cells. Supernatants of the indicated 161P2F20b-expressing and non-expressing cell lines were analyzed for for shedding/secretion of 161P2F10b protein by a capture ELISA. The capture ELISA was made using a 161P2F10b-specific MAb as the bottom capture MAb (1 ug/well), and X41.29 as the top detection MAb (2 ug/ml), and an anti-mouse IgG2a-HRP secondary and tetramethylbenzamidine as substrate for development. Recombinant 161P2F10b Tag5 ECD protein was used as a standard. 161P2F10b protein was detected in the media from 769 and Caki kidney cancer cells engineered to express 161P2F10b but not in the parental lines, indicating that 161P2F10b protein is shed or secreted. Shed/secreted 161P2F10b may exert its activity on cells in an autocrine/paracrine manner. In addition, shed/secreted 161P2F10b is useful as a diagnostic marker for 161P2F10b-expressing cancer and/or other 161P2F10b-expressing diseased tissues.

FIG. 43. Detection of secreted 161P2F10B in the serum of mice bearing UGK3 human kidney cancer xenografts. SCID mice inoculated subcutaneously with UGK3 kidney cancer cells were monitored for tumor growth (1 dimensional tumor measurements) and 161P2F10b serum levels (by capture ELISA) over the indicated times. The data demonstrates that 161P2F10b serum levels increase as the tumor size increases. This demonstrates that 161P2F10b is shed/secreted from 161P2F10b-expressing tissues in vivo and further demonstrates the utility of an ELISA to monitor 161P2F10b as a diagnostic marker.

FIG. 44: Detection of 161P2F10B protein by immunohistochemistry in kidney cancer patient specimens. Renal clear cell carcinoma tissue and its matched normal adjacent tissue as well as its metastatic cancer to lymph node were obtained from a kidney cancer patient. Frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes. The sections were then incubated with PE-labeled mouse monoclonal anti-ENPP3 antibody (Coulter-Immunotech, Marseilles, France) for 3 hours (FIG. 44 panels A–F), or isotype control antibody (FIG. 44 panels G-1). The slides were washed three times in buffer, and either analyzed by fluorescence microscopy (FIG. 44 panels A, B and C), or further incubated with DAKO EnVision+™ peroxidase-conjugated goat anti-mouse secondary antibody (DAKO Corporation, Carpenteria, Calif.) for 1 hour (FIG. 44 panels D, E, and F). The sections were then washed in buffer, developed using the DAB kit (SIGMA Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy (FIG. 44 panels D, E and F). The results showed strong expression of 161P2F10B in the renal carcinoma patient tissue (FIG. 44 panels A and D) and the kidney cancer metastasis to lymph node tissue (FIG. 44 panels C and F), but weakly in normal kidney (FIG. 44B and E). The expression was detected mostly around the cell membrane indicating that 161P2F10B is membrane associated in kidney cancer tissues. The weak expression detected in normal kidney was localized to the kidney tubules. The sections stained with the isotype control antibody were negative showing the specificity of the anti-ENPP3 antibody (FIG. 44 panels G-1).

FIG. 45: Expression of 161P2F10B in Human Patient Cancers by Western Blot. Cell lysates from kidney cancer tissues (KiCa), kidney cancer metastasis to lymph node (KiCa Met), as well as normal kidney (NK) were subjected to Western analysis using an anti-161P2F10B mouse monoclonal antibody. Briefly, tissues (−25 μg total protein) were solubilized in SDS-PAGE sample buffer and separated on a 10–20% SDS-PAGE gel and transferred to nitrocellulose. Blots were blocked in Tris-buffered saline (TBS)+3% non-fat milk and then probed with purified anti-161P2F10B antibody in TBS+0.15% Tween-20+1% milk. Blots were then washed and incubated with a 1:4,000 dilution of anti-mouse IgG-HRP conjugated secondary antibody. Following washing, anti-161P2F10B immunoreactive bands were developed and visualized by enhanced chemiluminescence and exposure to autoradiographic film. The specific anti-161P2F10B immunoreactive bands represent a monomeric form of the 161P2F10B protein, which runs at approximately 130 kDa. These results demonstrate that 161P2F10B is useful as a diagnostic and therapeutic target for kidney cancers, metastatic cancers and other such as tose aas listed in Table I and other human cancers that express 161P2F10B.

FIG. 46: Expression of 161P2F10B in Human Xenograft Tissues by Western Blot. Cell lysates from kidney cancer xenograft (KiCa Xeno), kidney cancer metastasis to lymph node xenograft (Met Xeno), as well as normal kidney (NK) were subjected to Western analysis using an anti-161P2F10B mouse monoclonal antibody. Briefly, tissues (−25 μg total protein) were solubilized in SDS-PAGE sample buffer and separated on a 10–20% SDS-PAGE gel and transferred to nitrocellulose. Blots were blocked in Tris-buffered saline (TBS)+3% non-fat milk and then probed with purified anti-161P2F10B antibody in TBS+0.15% Tween-20+1% milk. Blots were then washed and incubated with a 1:4,000 dilution of anti-mouse IgG-HRP conjugated secondary antibody. Following washing, anti-161P2F10B immunoreactive bands were developed and visualized by enhanced chemiluminescence and exposure to autoradiographic film. The specific anti-161P2F10B immunoreactive bands represent a monomeric form of the 161P2F10B protein, which runs at approximately 130 kDa, and a multimer of approximately 260 kDa. These results demonstrate that the human cancer xenograft mouse models can be used to study the diagnostic and therapeutic effects of 161P2F10B.

DETAILED DESCRIPTION OF THE INVENTION

Outline of Sections

I.) Definitions

II.) 161P2F10B Polynucleotides

II.A.) Uses of 161P2F10B Polynucleotides

II.A.1.) Monitoring of Genetic Abnormalities

II.A.2.) Antisense Embodiments

II.A.3.) Primers and Primer Pairs

II.A.4.) Isolation of 161P2F10B-Encoding Nucleic Acid Molecules

II.A.5.) Recombinant Nucleic Acid Molecules and Host-Vector Systems

III.) 161P2F10B-related Proteins

-   -   III.A.) Motif-bearing Protein Embodiments     -   III.B.) Expression of 161P2F10B-related Proteins     -   III.C.) Modifications of 161P2F10B-related Proteins     -   III.D.) Uses of 161P2F10B-related Proteins

IV.) 161P2F10B Antibodies

V.) 161P2F10B Cellular Immune Responses

VI.) 161P2F10B Transgenic Animals

VII.) Methods for the Detection of 161P2F10B

VIII.) Methods for Monitoring the Status of 161P2F10B-related Genes and Their Products

IX.) Identification of Molecules That Interact With 161P2F10B

X.) Therapeutic Methods and Compositions

-   -   X.A.) Anti-Cancer Vaccines

X.B.) 161P2F10B as a Target for Antibody-Based Therapy

X.C.) 161P2F10B as a Target for Cellular Immune Responses

-   -   X.C.1. Minigene Vaccines     -   X.C.2. Combinations of CTL Peptides with Helper Peptides     -   X.C.3. Combinations of CTL Peptides with T Cell Priming Agents     -   X.C.4. Vaccine Compositions Comprising DC Pulsed with CTL and/or         HTL Peptides     -   X.D.) Adoptive Immunotherapy

X.E.) Administration of Vaccines for Therapeutic or Prophylactic Purposes

XI.) Diagnostic and Prognostic Embodiments of 161P2F10B.

XII.) Inhibition of 161P2F10B Protein Function

-   -   XII.A.) Inhibition of 161P2F10B With Intracellular Antibodies     -   XII.B.) Inhibition of 161P2F10B with Recombinant Proteins     -   XII.C.) Inhibition of 161P2F10B Transcription or Translation     -   XII.D.) General Considerations for Therapeutic Strategies

XIII.) Identification, Characterization and Use of Modulators of 161P2F10b

XIV.) KITS/Articles of Manufacture

I.) Definitions:

Unless otherwise defined, all terms of art, notations and other scientific terms or terminology used herein are intended to have the meanings commonly understood by those of skill in the art to which this invention pertains. In some cases, terms with commonly understood meanings are defined herein for clarity and/or for ready reference, and the inclusion of such definitions herein should not necessarily be construed to represent a substantial difference over what is generally understood in the art. Many of the techniques and procedures described or referenced herein are well understood and commonly employed using conventional methodology by those skilled in the art, such as, for example, the widely utilized molecular cloning methodologies described in Sambrook et al., Molecular Cloning: A Laboratory Manual 2nd. edition (1989) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. As appropriate, procedures involving the use of commercially available kits and reagents are generally carried out in accordance with manufacturer defined protocols and/or parameters unless otherwise noted.

The terms “advanced prostate cancer”, “locally advanced prostate cancer”, “advanced disease” and “locally advanced disease” mean prostate cancers that have extended through the prostate capsule, and are meant to include stage C disease under the American Urological Association (AUA) system, stage C1–C2 disease under the Whitmore-Jewelt system, and stage T3–T4 and N+ disease under the TNM (tumor, node, metastasis) system. In general, surgery is not recommended for patients with locally advanced disease, and these patients have substantially less favorable outcomes compared to patients having clinically localized (organ-confined) prostate cancer. Locally advanced disease is clinically identified by palpable evidence of induration beyond the lateral border of the prostate, or asymmetry or induration above the prostate base. Locally advanced prostate cancer is presently diagnosed pathologically following radical prostatectomy if the tumor invades or penetrates the prostatic capsule, extends into the surgical margin, or invades the seminal vesicles.

“Altering the native glycosylation pattern” is intended for purposes herein to mean deleting one or more carbohydrate moieties found in native sequence 161P2F10B (either by removing the underlying glycosylation site or by deleting the glycosylation by chemical and/or enzymatic means), and/or adding one or more glycosylation sites that are not present in the native sequence 161P2F10B. In addition, the phrase includes qualitative changes in the glycosylation of the native proteins, involving a change in the nature and proportions of the various carbohydrate moieties present.

The term “analog” refers to a molecule which is structurally similar or shares similar or corresponding attributes with another molecule (eg. a 161P2F10B-related protein). For example, an analog of a 161P2F10B protein can be specifically bound by an antibody or T cell that specifically binds to 161P2F10B.

The term “antibody” is used in the broadest sense. Therefore, an “antibody” can be naturally occurring or man-made such as monoclonal antibodies produced by conventional hybridoma technology. Anti-1611P2F10B antibodies comprise monoclonal and polyclonal antibodies as well as fragments containing the antigen-binding domain and/or one or more complementarity determining regions of these antibodies.

An “antibody fragment” is defined as at least a portion of the variable region of the immunoglobulin molecule that binds to its target, i.e., the antigen-binding region. In one embodiment it specifically covers single anti-161P2F10B antibodies and clones thereof (including agonist, antagonist and neutralizing antibodies) and anti-161 P2F10B antibody compositions with polyepitopic specificity.

The term “codon optimized sequences” refers to nucleotide sequences that have been optimized for a particular host species by replacing any codons having a usage frequency of less than about 20%. Nucleotide sequences that have been optimized for expression in a given host species by elimination of spurious polyadenylation sequences, elimination of exonaintron splicing signals, elimination of transposon-like repeats and/or optimization of GC content in addition to codon optimization are referred to herein as an “expression enhanced sequences.”

A “combinatorial library” is a collection of diverse chemical compounds generated by either chemical synthesis or biological synthesis by combining a number of chemical “building blocks” such as reagents. For example, a linear combinatorial chemical library, such as a polypeptide (e.g., mutein) library, is formed by combining a set of chemical building blocks called amino acids in every possible way for a given compound length (i.e., the number of amino acids in a polypeptide compound). Numerous chemical compounds are synthesized through such combinatorial mixing of chemical building blocks (Gallop et al., J. Med. Chem. 37(9): 1233–1251 (1994)).

Preparation and screening of combinatorial libraries is well known to those of skill in the art. Such combinatorial chemical libraries include, but are not limited to, peptide libraries (see, e.g., U.S. Pat. No. 5,010,175, Furka, Pept. Prot. Res. 37:487–493 (1991), Houghton et al., Nature, 354:84–88 (1991)), peptoids (PCT Publication No WO 91/19735), encoded peptides (PCT Publication WO 93/20242), random bio-oligomers (PCT Publication WO 92/00091), benzodiazepines (U.S. Pat. No. 5,288,514), diversomers such as hydantoins, benzodiazepines and dipeptides (Hobbs et al., Proc. Nat. Acad. Sci. USA 90:6909–6913 (1993)), vinylogous polypeptides (Hagihara et al., J. Amer. Chem. Soc. 114:6568 (1992)), nonpeptidal peptidomimetics with a Beta-D-Glucose scaffolding (Hirschmann et al., J. Amer. Chem. Soc. 114:9217–9218 (1992)), analogous organic syntheses of small compound libraries (Chen et al., J. Amer. Chem. Soc. 116:2661 (1994)), oligocarbamates (Cho, et al., Science 261:1303 (1993)), and/or peptidyl phosphonates (Campbell et al., J. Org. Chem. 59:658 (1994)). See, generally, Gordon et al., J. Med. Chem. 37:1385 (1994), nucleic acid libraries (see, e.g., Stratagene, Corp.), peptide nucleic acid libraries (see, e.g., U.S. Pat. No. 5,539,083), antibody libraries (see, e.g., Vaughn et al., Nature Biotechnology 14(3): 309–314 (1996), and PCT/US96/10287), carbohydrate libraries (see, e.g., Liang et al., Science 274:1520–1522 (1996), and U.S. Pat. No. 5,593,853), and small organic molecule libraries (see, e.g., benzodiazepines, Baum, C&EN, January 18, page 33 (1993); isoprenoids, U.S. Pat. No. 5,569,588; thiazolidinones and metathiazanones, U.S. Pat. No. 5,549,974; pyrrolidines, U.S. Pat. Nos. 5,525,735 and 5,519,134; morpholino compounds, U.S. Pat. No. 5,506, 337; benzodiazepines, U.S. Pat. No. 5,288,514; and the like).

Devices for the preparation of combinatorial libraries are commercially available (see, e.g., 357 NIPS, 390 NIPS, Advanced Chem Tech, Louisville Ky.; Symphony, Rainin, Woburn, Mass.; 433A, Applied Biosystems, Foster City, Calif.; 9050, Plus, Millipore, Bedford, Mass.). A number of well-known robotic systems have also been developed for solution phase chemistries. These systems include automated workstations such as the automated synthesis apparatus developed by Takeda Chemical Industries, LTD. (Osaka, Japan) and many robotic systems utilizing robotic arms (Zymate H, Zymark Corporation, Hopkinton, Mass.; Orca, Hewlett-Packard, Palo Alto, Calif.), which mimic the manual synthetic operations performed by a chemist. Any of the above devices are suitable for use with the present invention. The nature and implementation of modifications to these devices (if any) so that they can operate as discussed herein will be apparent to persons skilled in the relevant art. In addition, numerous combinatorial libraries are themselves commercially available (see, e.g., ComGenex, Princeton, N.J.; Asinex, Moscow, RU; Tnpos, Inc., St. Louis, Mo.; ChemStar, Ltd, Moscow, RU; 3D Pharmaceuticals, Exton, Pa.; Martek Biosciences, Columbia, Md.; etc.).

The term “cytotoxic agent” refers to a substance that inhibits or prevents the expression activity of cells, function of cells and/or causes destruction of cells. The term is intended to include radioactive isotopes chemotherapeutic agents, and toxins such as small molecule toxins or enzymatically active toxins of bacterial, fungal, plant or animal origin, including fragments and/or variants thereof. Examples of cytotoxic agents include, but are not limited to auristatins, auromycins, maytansinoids, yttrium, bismuth, ricin, ricin A-chain, combrestatin, duocarmycins, dolostatins, doxorubicin, daunorubicin, taxol, cisplatin, cc1065, ethidium bromide, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicine, dihydroxy anthracin dione, actinomycin, diphtheria toxin, Pseudomonas exotoxin (PE) A, PE40, abrin, abrin A chain, modeccin A chain, alpha-sarcin, gelonin, mitogellin, retstrictocin, phenomycin, enomycin, curicin, crotin, calicheamicin, Sapaonaria officinalis inhibitor, and glucocorticoid and other chemotherapeutic agents, as well as radioisotopes such as At²¹¹, I¹³¹, I¹²⁵, Y⁹⁰, Re¹⁸⁶, Re¹⁸⁸, Sm¹⁵³, Bi^(212 or 213), P³² and radioactive isotopes of Lu including Lu¹⁷⁷. Antibodies may also be conjugated to an anti-cancer pro-drug activating enzyme capable of converting the pro-drug to its active form.

The “gene product” is sometimes referred to herein as a protein or mRNA. For example, a “gene product of the invention” is sometimes referred to herein as a “cancer amino acid sequence”, “cancer protein”, “protein of a cancer listed in Table I”, a “cancer mRNA”, “mRNA of a cancer listed in Table I”, etc. In one embodiment, the cancer protein is encoded by a nucleic acid of FIG. 2. The cancer protein can be a fragment, or alternatively, be the full-length protein to the fragment encoded by the nucleic acids of FIG. 2. In one embodiment, a cancer amino acid sequence is used to determine sequence identity or similarity. In another embodiment, the sequences are naturally occurring allelic variants of a protein encoded by a nucleic acid of FIG. 2. In another embodiment, the sequences are sequence variants as further described herein.

“High throughput screening” assays for the presence, absence, quantification, or other properties of particular nucleic acids or protein products are well known to those of skill in the art. Similarly, binding assays and reporter gene assays are similarly well known. Thus, e.g., U.S. Pat. No. 5,559,410 discloses high throughput screening methods for proteins; U.S. Pat. No. 5,585,639 discloses high throughput screening methods for nucleic acid binding (i.e., in arrays); while U.S. Pat. Nos. 5,576,220 and 5,541,061 disclose high throughput methods of screening for ligand/antibody binding.

In addition, high throughput screening systems are commercially available (see, e.g., Amersham Biosciences, Piscataway, N.J.; Zymark Corp., Hopkinton, Mass.; Air Technical Industries, Mentor, Ohio; Beckman Instruments, Inc. Fullerton, Calif.; Precision Systems, Inc., Natick, Mass.; etc.). These systems typically automate entire procedures, including all sample and reagent pipetting, liquid dispensing, timed incubations, and final readings of the microplate in detector(s) appropriate for the assay. These configurable systems provide high throughput and rapid start up as well as a high degree of flexibility and customization. The manufacturers of such systems provide detailed protocols for various high throughput systems. Thus, e.g., Zymark Corp. provides technical bulletins describing screening systems for detecting the modulation of gene transcription, ligand binding, and the like.

The term “homolog” refers to a molecule which exhibits homology to another molecule, by for example, having sequences of chemical residues that are the same or similar at corresponding positions.

“Human Leukocyte Antigen” or “HLA” is a human class I or class II Major Histocompatibility Complex (MHC) protein (see, e.g., Stites, et al., IMMUNOLOGY, 8TH ED., Lange Publishing, Los Altos, Calif. (1994).

The terms “hybridize”, “hybridizing”, “hybridizes” and the like, used in the context of polynucleotides, are meant to refer to conventional hybridization conditions, preferably such as hybridization in 50% formamide/6×SSC/0.1% SDS/100 μg/ml ssDNA, in which temperatures for hybridization are above 37 degrees C. and temperatures for washing in 0.1×SSC/0.1% SDS are above 55 degrees C.

The phrases “isolated” or “biologically pure” refer to material which is substantially or essentially free from components which normally accompany the material as it is found in its native state. Thus, isolated peptides in accordance with the invention preferably do not contain materials normally associated with the peptides in their in situ environment. For example, a polynucleotide is said to be “isolated” when it is substantially separated from contaminant polynucleotides that correspond or are complementary to genes other than the 161P2F10B genes or that encode polypeptides other than 161P2F10B gene product or fragments thereof. A skilled artisan can readily employ nucleic acid isolation procedures to obtain an isolated 161P2F10B polynucleotide. A protein is said to be “isolated,” for example, when physical, mechanical or chemical methods are employed to remove the 161P2F10B proteins from cellular constituents that are normally associated with the protein. A skilled artisan can readily employ standard purification methods to obtain an isolated 161P2F10B protein. Alternatively, an isolated protein can be prepared by chemical means.

The term “mammal” refers to any organism classified as a mammal, including mice, rats, rabbits, dogs, cats, cows, horses and humans. In one embodiment of the invention, the mammal is a mouse. In another embodiment of the invention, the mammal is a human.

The terms “metastatic prostate cancer” and “metastatic disease” mean prostate cancers that have spread to regional lymph nodes or to distant sites, and are meant to include stage D disease under the AUA system and stage T×N×M+ under the TNM system. As is the case with locally advanced prostate cancer, surgery is generally not indicated for patients with metastatic disease, and hormonal (androgen ablation) therapy is a preferred treatment modality. Patients with metastatic prostate cancer eventually develop an androgen-refractory state within 12 to 18 months of treatment initiation. Approximately half of these androgen-refractory patients die within 6 months after developing that status. The most common site for prostate cancer metastasis is bone. Prostate cancer bone metastases are often osteoblastic rather than osteolytic (i.e., resulting in net bone formation). Bone metastases are found most frequently in the spine, followed by the femur, pelvis, rib cage, skull and humerus. Other common sites for metastasis include lymph nodes, lung, liver and brain. Metastatic prostate cancer is typically diagnosed by open or laparoscopic pelvic lymphadenectomy, whole body radionuclide scans, skeletal radiography, and/or bone lesion biopsy.

The term “modulator” or “test compound” or “drug candidate” or grammatical equivalents as used herein describe any molecule, e.g., protein, oligopeptide, small organic molecule, polysaccharide, polynucleotide, etc., to be tested for the capacity to directly or indirectly alter the cancer phenotype or the expression of a cancer sequence, e.g., a nucleic acid or protein sequences, or effects of cancer sequences (e.g., signaling, gene expression, protein interaction, etc.) In one aspect, a modulator will neutralize the effect of a cancer protein of the invention. By “neutralize” is meant that an activity of a protein is inhibited or blocked, along with the consequent effect on the cell. In another aspect, a modulator will neutralize the effect of a gene, and its corresponding protein, of the invention by normalizing levels of said protein. In preferred embodiments, modulators alter expression profiles, or expression profile nucleic acids or proteins provided herein, or downstream effector pathways. In one embodiment, the modulator suppresses a cancer phenotype, e.g. to a normal issue fingerprint. In another embodiment, a modulator induced a cancer phenotype. Generally, a plurality of assay mixtures is run in parallel with different agent concentrations to obtain a differential response to the various concentrations. Typically, one of these concentrations serves as a negative control, i.e., at zero concentration or below the level of detection.

Modulators, drug candidates or test compounds encompass numerous chemical classes, though typically they are organic molecules, preferably small organic compounds having a molecular weight of more than 100 and less than about 2,500 Daltons. Preferred small molecules are less than 2000, or less than 1500 or less than 1000 or less than 500 D. Candidate agents comprise functional groups necessary for structural interaction with proteins, particularly hydrogen bonding, and typically include at least an amine, carbonyl, hydroxyl or carboxyl group, preferably at least two of the functional chemical groups. The candidate agents often comprise cyclical carbon or heterocyclic structures and/or aromatic or polyaromatic structures substituted with one or more of the above functional groups. Modulators also comprise biomolecules such as peptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof. Particularly preferred are peptides. One class of modulators are peptides, for example of from about five to about 35 amino acids, with from about five to about 20 amino acids being preferred, and from about 7 to about 15 being particularly preferred. Preferably, the cancer modulatory protein is soluble, includes a non-transmembrane region, and/or, has an N-terminal Cys to aid in solubility. In one embodiment, the C-terminus of the fragment is kept as a free acid and the N-terminus is a free amine to aid in coupling, i.e., to cysteine. In one embodiment, a cancer protein of the invention is conjugated to an immunogenic agent as discussed herein. In one embodiment, the cancer protein is conjugated to BSA. The peptides of the invention, e.g., of preferred lengths, can be linked to each other or to other amino acids to create a longer peptide/protein. The modulatory peptides can be digests of naturally occurring proteins as is outlined above, random peptides, or “biased” random peptides. In a preferred embodiment, peptide/protein-based modulators are antibodies, and fragments thereof, as defined herein.

Modulators of cancer can also be nucleic acids. Nucleic acid modulating agents can be naturally occurring nucleic acids, random nucleic acids, or “biased” random nucleic acids. For example, digests of prokaryotic or eukaryotic genomes can be used in an approach analogous to that outlined above for proteins.

The term “monoclonal antibody” refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the antibodies comprising the population are identical except for possible naturally occurring mutations that are present in minor amounts.

A “motif”, as in biological motif of a 161P2F10B-related protein, refers to any pattern of amino acids forming part of the primary sequence of a protein, that is associated with a particular function (e.g. protein-protein interaction, protein-DNA interaction, etc) or modification (e.g. that is phosphorylated, glycosylated or amidated), or localization (e.g. secretory sequence, nuclear localization sequence, etc.) or a sequence that is correlated with being immunogenic, either humorally or cellularly. A motif can be either contiguous or capable of being aligned to certain positions that are generally correlated with a certain function or property. In the context of HLA motifs, “motif” refers to the pattern of residues in a peptide of defined length, usually a peptide of from about 8 to about 13 amino acids for a class I HLA motif and from about 6 to about 25 amino acids for a class II HLA motif, which is recognized by a particular HLA molecule. Peptide motifs for HLA binding are typically different for each protein encoded by each human HLA allele and differ in the pattern of the primary and secondary anchor residues.

A “pharmaceutical excipient” comprises a material such as an adjuvant, a carrier, pH-adjusting and buffering agents, tonicity adjusting agents, wetting agents, preservative, and the like.

“Pharmaceutically acceptable” refers to a non-toxic, inert, and/or composition that is physiologically compatible with humans or other mammals.

The term “polynucleotide” means a polymeric form of nucleotides of at least 10 bases or base pairs in length, either ribonucleotides or deoxynucleotides or a modified form of either type of nucleotide, and is meant to include single and double stranded forms of DNA and/or RNA. In the art, this term if often used interchangeably with “oligonucleotide”. A polynucleotide can comprise a nucleotide sequence disclosed herein wherein thymidine (T), as shown for example in FIG. 2, can also be uracil (U); this definition pertains to the differences between the chemical structures of DNA and RNA, in particular the observation that one of the four major bases in RNA is uracil (U) instead of thymidine (T).

The term “polypeptide” means a polymer of at least about 4, 5, 6, 7, or 8 amino acids. Throughout the specification, standard three letter or single letter designations for amino acids are used. In the art, this term is often used interchangeably with “peptide” or “protein”.

An HLA “primary anchor residue” is an amino acid at a specific position along a peptide sequence which is understood to provide a contact point between the immunogenic peptide and the HLA molecule. One to three, usually two, primary anchor residues within a peptide of defined length generally defines a “motif” for an immunogenic peptide. These residues are understood to fit in close contact with peptide binding groove of an HLA molecule, with their side chains buried in specific pockets of the binding groove. In one embodiment, for example, the primary anchor residues for an HLA class I molecule are located at position 2 (from the amino terminal position) and at the carboxyl terminal position of a 8, 9, 10, 11, or 12 residue peptide epitope in accordance with the invention. Alternatively, in another embodiment, the primary anchor residues of a peptide binds an HLA class II molecule are spaced relative to each other, rather than to the termini of a peptide, where the peptide is generally of at least 9 amino acids in length. The primary anchor positions for each motif and supermotif are set forth in Table IV. For example, analog peptides can be created by altering the presence or absence of particular residues in the primary and/or secondary anchor positions shown in Table IV. Such analogs are used to modulate the binding affinity and/or population coverage of a peptide comprising a particular HLA motif or supermotif.

“Radioisotopes” include, but are not limited to the following (non-limiting exemplary uses are also set forth):

-   Examples of Medical Isotopes: -   Isotope -   Description of use -   Actinium-225 -   (AC-225) -   See Thorium-229 (Th-229) -   Actinium-227 -   (AC-227) -   Parent of Radium-223 (Ra-223) which is an alpha emitter used to     treat metastases in the skeleton resulting from cancer (i.e., breast     and prostate cancers), and cancer radioimmunotherapy -   Bismuth-212 -   (Bi-212) -   See Thorium-228 (Th-228) -   Bismuth-213 -   (Bi-213) -   See Thorium-229 (Th-229) -   Cadmium-109 -   (Cd-109) -   Cancer detection -   Cobalt-60 -   (Co-60) -   Radiation source for radiotherapy of cancer, for food irradiators,     and for sterilization of medical supplies -   Copper-64 -   (Cu-64) -   A positron emitter used for cancer therapy and SPECT imaging -   Copper-67 -   (Cu-67) -   Beta/gamma emitter used in cancer radioimmunotherapy and diagnostic     studies (i.e., breast and colon cancers, and lymphoma) -   Dysprosium-166 -   (Dy-166) -   Cancer radioimmunotherapy -   Erbium-169 -   (Er-169) -   Rheumatoid arthritis treatment, particularly for the small joints     associated with fingers and toes -   Europium-152 -   (Eu-152) -   Radiation source for food irradiation and for sterilization of     medical supplies -   Europium-154 -   (Eu-154) -   Radiation source for food irradiation and for sterilization of     medical supplies -   Gadolinium-153 -   (Gd-153) -   Osteoporosis detection and nuclear medical quality assurance devices -   Gold-198 -   (Au-198) -   Implant and intracavity therapy of ovarian, prostate, and brain     cancers -   Holmium-166 -   (Ho-166) -   Multiple myeloma treatment in targeted skeletal therapy, cancer     radioimmunotherapy, bone marrow ablation, and rheumatoid arthritis     treatment -   Iodine-125 -   (1–125) -   Osteoporosis detection, diagnostic imaging, tracer drugs, brain     cancer treatment, radiolabeling, tumor imaging, mapping of receptors     in the brain, interstitial radiation therapy, brachytherapy for     treatment of prostate cancer, determination of glomerular filtration     rate (GFR), determination of plasma volume, detection of deep vein     thrombosis of the legs -   Iodine-131 -   (I-131) -   Thyroid function evaluation, thyroid disease detection, treatment of     thyroid cancer as well as other non-malignant thyroid diseases     (i.e., Graves disease, goiters, and hyperthyroidism), treatment of     leukemia, lymphoma, and other forms of cancer (e.g., breast cancer)     using radioimmunotherapy -   Iridium-192 -   (Ir-192) -   Brachytherapy, brain and spinal cord tumor treatment, treatment of     blocked arteries (i.e., arteriosclerosis and restenosis), and     implants for breast and prostate tumors -   Lutetium-177 -   (Lu-177) -   Cancer radioimmunotherapy and treatment of blocked arteries (i.e.,     arteriosclerosis and restenosis) -   Molybdenum-99 -   (Mo-99) -   Parent of Technetium-99m (Tc-99m) which is used for imaging the     brain, liver, lungs, heart, and other organs. Currently, Tc-99m is     the most widely used radioisotope used for diagnostic imaging of     various cancers and diseases involving the brain, heart, liver,     lungs; also used in detection of deep vein thrombosis of the legs -   Osmium-194 -   (Os-194) -   Cancer radioimmunotherapy -   Palladium-103 -   (Pd-103) -   Prostate cancer treatment -   Platinum-195m -   (Pt-195m) -   Studies on biodistribution and metabolism of cisplatin, a     chemotherapeutic drug -   Phosphorus-32 -   (P-32) -   Polycythemia rubra vera (blood cell disease) and leukemia treatment,     bone cancer diagnosis/treatment; colon, pancreatic, and liver cancer     treatment; radiolabeling nucleic acids for in vitro research,     diagnosis of superficial tumors, treatment of blocked arteries     (i.e., arteriosclerosis and restenosis), and intracavity therapy -   Phosphorus-33 -   (P-33) -   Leukemia treatment, bone disease diagnosis/treatment, radiolabeling,     and treatment of blocked arteries (i.e., arteriosclerosis and     restenosis) -   Radium-223 -   (Ra-223) -   See Actinium-227 (Ac-227) -   Rhenium-186 -   (Re-186) -   Bone cancer pain relief, rheumatoid arthritis treatment, and     diagnosis and treatment of lymphoma and bone, breast, colon, and     liver cancers using radioimmunotherapy -   Rhenium-188 -   (Re-188) -   Cancer diagnosis and treatment using radioimmunotherapy, bone cancer     pain relief, treatment of rheumatoid arthritis, and treatment of     prostate cancer -   Rhodium-105 -   (Rh-105) -   Cancer radioimmunotherapy -   Samarium-145 -   (Sm-145) -   Ocular cancer treatment -   Samarium-153 -   (Sm-153) -   Cancer radioimmunotherapy and bone cancer pain relief -   Scandium-47 -   (Sc-47) -   Cancer radioimmunotherapy and bone cancer pain relief -   Selenium-75 -   (Se-75) -   Radiotracer used in brain studies, imaging of adrenal cortex by     gamma-scintigraphy, lateral locations of steroid secreting tumors,     pancreatic scanning, detection of hyperactive parathyroid glands,     measure rate of bile acid loss from the endogenous pool -   Strontium-85 -   (Sr-85) -   Bone cancer detection and brain scans -   Strontium-89 -   (Sr-89) -   Bone cancer pain relief, multiple myeloma treatment, and     osteoblastic therapy -   Technetium-99m -   (Tc-99m) -   See Molybdenum-99 (Mo-99) -   Thorium-228 -   (Th-228) -   Parent of Bismuth-212 (Bi-212) which is an alpha emitter used in     cancer radioimmunotherapy -   Thorium-229 -   (Th-229) -   Parent of Actinium-225 (Ac-225) and grandparent of Bismuth-213     (Bi-213) which are alpha emitters used in cancer radioimmunotherapy -   Thulium-170 -   (Tm-170) -   Gamma source for blood irradiators, energy source for implanted     medical devices -   Tin-117m -   (Sn-117m) -   Cancer immunotherapy and bone cancer pain relief -   Tungsten-188 -   (W-188) -   Parent for Rhenium-188 (Re-188) which is used for cancer     diagnostics/treatment, bone cancer pain relief, rheumatoid arthritis     treatment, and treatment of blocked arteries (i.e., arteriosclerosis     and restenosis) -   Xenon-127 -   (Xe-127) -   Neuroimaging of brain disorders, high resolution SPECT studies,     pulmonary function tests, and cerebral blood flow studies -   Ytterbium-175 -   (Yb-175) -   Cancer radioimmunotherapy -   Yttrium-90 -   (Y-90) -   Microseeds obtained from irradiating Yttrium-89 (Y-89) for liver     cancer treatment -   Yttrium-91 -   (Y-91) -   A gamma-emitting label for Yttrium-90 (Y-90) which is used for     cancer radioimmunotherapy (i.e., lymphoma, breast, colon, kidney,     lung, ovarian, prostate, pancreatic, and inoperable liver cancers)

By “randomized” or grammatical equivalents as herein applied to nucleic acids and proteins is meant that each nucleic acid and peptide consists of essentially random nucleotides and amino acids, respectively. These random peptides (or nucleic acids, discussed herein) can incorporate any nucleotide or amino acid at any position. The synthetic process can be designed to generate randomized proteins or nucleic acids, to allow the formation of all or most of the possible combinations over the length of the sequence, thus forming a library of randomized candidate bioactive proteinaceous agents.

In one embodiment, a library is “fully randomized,” with no sequence preferences or constants at any position. In another embodiment, the library is a “biased random” library. That is, some positions within the sequence either are held constant, or are selected from a limited number of possibilities. For example, the nucleotides or amino acid residues are randomized within a defined class, e.g., of hydrophobic amino acids, hydrophilic residues, sterically biased (either small or large) residues, towards the creation of nucleic acid binding domains, the creation of cysteines, for cross-linking, prolines for SH-3 domains, serines, threonines, tyrosines or histidines for phosphorylation sites, etc., or to purines, etc.

A “recombinant DNA or RNA molecule is a DNA or RNA molecule that has been subjected to molecular manipulation in vitro.

Non-limiting examples of small molecules include compounds that bind or interact with 161P2F10B, ligands including hormones, neuropeptides, chemokines, odorants, phospholipids, and functional equivalents thereof that bind and preferably inhibit 161P2F10B protein function. Such non-limiting small molecules preferably have a molecular weight of less than about 10 kDa, more preferably below about 9, about 8, about 7, about 6, about 5 or about 4 kDa. In certain embodiments, small molecules physically associate with, or bind, 161P2F10B protein; are not found in naturally occurring metabolic pathways; and/or are more soluble in aqueous than non-aqueous solutions

“Stringency” of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures. Hybridization generally depends on the ability of denatured nucleic acid sequences to reanneal when complementary strands are present in an environment below their melting temperature. The higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature that can be used. As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. For additional details and explanation of stringency of hybridization reactions, see Ausubel et al., Current Protocols in Molecular Biology, Wiley Interscience Publishers, (1995).

“Stringent conditions” or “high stringency conditions”, as defined herein, are identified by, but not limited to, those that: (1) employ low ionic strength and high temperature for washing, for example 0.015 M sodium chloride/0.0015 M sodium citrate/0.1% sodium dodecyl sulfate at 50° C.; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (v/v) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42° C.; or (3) employ 50% formamide, 5×SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5× Denhardt's solution, sonicated salmon sperm DNA (50 μg/ml), 0.1% SDS, and 10% dextran sulfate at 42° C., with washes at 420C in 0.2×SSC (sodium chloride/sodium. citrate) and 50% formamide at 55° C., followed by a high-stringency wash consisting of 0.1×SSC containing EDTA at 55° C. “Moderately stringent conditions” are described by, but not limited to, those in Sambrook et al., Molecular Cloning: A Laboratory Manual, New York: Cold Spring Harbor Press, 1989, and include the use of washing solution and hybridization conditions (e.g., temperature, ionic strength and % SDS) less stringent than those described above. An example of moderately stringent conditions is overnight incubation at 37° C. in a solution comprising: 20% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5× Denhardt's solution, 10% dextran sulfate, and 20 mg/mL denatured sheared salmon sperm DNA, followed by washing the filters in 1×SSC at about 37–50° C. The skilled artisan will recognize how to adjust the temperature, ionic strength, etc. as necessary to accommodate factors such as probe length and the like.

An HLA “supermotif” is a peptide binding specificity shared by HLA molecules encoded by two or more HLA alleles. Overall phenotypic frequencies of HLA-supertypes in different ethnic populations are set forth in Table IV (F). The non-limiting constituents of various supetypes are as follows:

A2: A*0201, A*0202, A*0203, A*0204, A* 0205, A*0206, A*6802, A*6901, A*0207

A3: A3, A11, A31,A*3301,A*6801, A*0301,A*1101,A*3101

B7: B7, B*3501–03, B*51, B*5301, B*5401, B*5501, B*5502, B*5601, B*6701, B*7801, B*0702, B*5101, B*5602

B44: B*3701, B*4402, B*4403, B*60 (B*4001), B61 (B*4006)

A1: A*0102, A*2604, A*3601, A*4301, A*8001

A24: A*24, A*30, A*2403, A*2404, A*3002, A*3003

B27: B*1401–02, B*1503, B*1509, B*1510, B*1518, B*3801–02, B*3901, B*3902, B*3903–04, B*4801–02, B*7301, B*2701–08

B58: B*1516, B*1517, B*5701, B*5702, B58

B62: B*4601, B52, B*1501 (B62), B*1502 (B75), B*1513 (B77)

Calculated population coverage afforded by different HLA-supertype combinations are set forth in Table IV (G).

As used herein “to treat” or “therapeutic” and grammatically related terms, refer to any improvement of any consequence of disease, such as prolonged survival, less morbidity, and/or a lessening of side effects which are the byproducts of an alternative therapeutic modality; full eradication of disease is not required.

A “transgenic animal” (e.g., a mouse or rat) is an animal having cells that contain a transgene, which transgene was introduced into the animal or an ancestor of the animal at a prenatal, e.g., an embryonic stage. A “transgene” is a DNA that is integrated into the genome of a cell from which a transgenic animal develops.

As used herein, an HLA or cellular immune response “vaccine” is a composition that contains or encodes one or more peptides of the invention. There are numerous embodiments of such vaccines, such as a cocktail of one or more individual peptides; one or more peptides of the invention comprised by a polyepitopic peptide; or nucleic acids that encode such individual peptides or polypeptides, e.g., a minigene that encodes a polyepitopic peptide. The “one or more peptides” can include any whole unit integer from 1–150 or more, e.g., at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, or 150 or more peptides of the invention. The peptides or polypeptides can optionally be modified, such as by lipidation, addition of targeting or other sequences. HLA class I peptides of the invention can be admixed with, or linked to, HLA class II peptides, to facilitate activation of both cytotoxic T lymphocytes and helper T lymphocytes. HLA vaccines can also comprise peptide-pulsed antigen presenting cells, e.g., dendritic cells.

The term “variant” refers to a molecule that exhibits a variation from a described type or norm, such as a protein that has one or more different amino acid residues in the corresponding position(s) of a specifically described protein (e.g. the 161P2F10B protein shown in FIG. 2 or FIG. 3. An analog is an example of a variant protein. Splice isoforms and single nucleotides polymorphisms (SNPs) are further examples of variants.

The “161P2F10B-related proteins” of the invention include those specifically identified herein, as well as allelic variants, conservative substitution variants, analogs and homologs that can be isolated/generated and characterized without undue experimentation following the methods outlined herein or readily available in the art. Fusion proteins that combine parts of different 161P2F10B proteins or fragments thereof, as well as fusion proteins of a 161P2F10B protein and a heterologous polypeptide are also included. Such 161P2F10B proteins are collectively referred to as the 161P2F10B-related proteins, the proteins of the invention, or 161P2F10B. The term “161P2F10B-related protein” refers to a polypeptide fragment or a 161P2F10B protein sequence of 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more than 25 amino acids; or, at least 30, 35, 40, 45, 50, 55, 60, 65, 70, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, or 664 or more amino acids.

II.) 161P2F10B Polynucleotides

One aspect of the invention provides polynucleotides corresponding or complementary to all or part of a 161P2F10B gene, mRNA, and/or coding sequence, preferably in isolated form, including polynucleotides encoding a 161P2F10B-related protein and fragments thereof, DNA, RNA, DNA/RNA hybrid, and related molecules, polynucleotides or oligonucleotides complementary to a 161P2F10B gene or mRNA sequence or a part thereof, and polynucleotides or oligonucleotides that hybridize to a 161P2F10B gene, mRNA, or to a 161P2F10B encoding polynucleotide (collectively, “161P2F10B polynucleotides”). In all instances when referred to in this section, T can also be U in FIG. 2.

Embodiments of a 161P2F10B polynucleotide include: a 161P2F10B polynucleotide having the sequence shown in FIG. 2, the nucleotide sequence of 161P2F10B as shown in FIG. 2 wherein T is U; at least 10 contiguous nucleotides of a polynucleotide having the sequence as shown in FIG. 2; or, at least 10 contiguous nucleotides of a polynucleotide having the sequence as shown in FIG. 2 where T is U. For example, embodiments of 161P2F10B nucleotides comprise, without limitation:

-   -   (I) a polynucleotide comprising, consisting essentially of, or         consisting of a sequence as shown in FIG. 2, wherein T can also         be U;     -   (II) a polynucleotide comprising, consisting essentially of, or         consisting of the sequence as shown in FIG. 2A, from nucleotide         residue number 44 through nucleotide residue number 2671,         including the stop codon, wherein T can also be U;     -   (III) a polynucleotide comprising, consisting essentially of, or         consisting of the sequence as shown in FIG. 2B, from nucleotide         residue number 44 through nucleotide residue number 2671,         including the stop codon, wherein T can also be U;     -   (IV) a polynucleotide comprising, consisting essentially of, or         consisting of the sequence as shown in FIG. 2C, from nucleotide         residue number 44 through nucleotide residue number 2671,         including the a stop codon, wherein T can also be U;     -   (V) a polynucleotide comprising, consisting essentially of, or         consisting of the sequence as shown in FIG. 2D, from nucleotide         residue number 44 through nucleotide residue number 2671,         including the stop codon, wherein T can also be U;     -   (VI) a polynucleotide comprising, consisting essentially of, or         consisting of the sequence as shown in FIG. 2E, from nucleotide         residue number 44 through nucleotide residue number 2671,         including the stop codon, wherein T can also be U;     -   (VII) a polynucleotide comprising, consisting essentially of, or         consisting of the sequence as shown in FIG. 2F, from nucleotide         residue number 84 through nucleotide residue number 2711,         including the stop codon, wherein T can also be U;     -   (VIII) a polynucleotide comprising, consisting essentially of,         or consisting of the sequence as shown in FIG. 2G, from         nucleotide residue number 276 through nucleotide residue number         2801, including the stop codon, wherein T can also be U;     -   (IX) a polynucleotide that encodes a 161P2F10B-related protein         that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100%         homologous to an entire amino acid sequence shown in FIGS. 2A–G;     -   (X) a polynucleotide that encodes a 161P2F10B-related protein         that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100%         identical to an entire amino acid sequence shown in FIGS. 2A–G;     -   (XI) a polynucleotide that encodes at least one peptide set         forth in Tables VIII–XXI and XXII–XLIX;     -   (XII) a polynucleotide that encodes a peptide region of at least         5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,         22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino         acids of a peptide of FIGS. 3A–D in any whole number increment         up to 875 that includes at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,         11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,         27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having         a value greater than 0.5 in the Hydrophilicity profile of FIG.         5;     -   (XIII) a polynucleotide that encodes a peptide region of at         least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,         21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino         acids of a peptide of FIGS. 3A–D in any whole number increment         up to 875 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,         13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,         29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value         less than 0.5 in the Hydropathicity profile of FIG. 6;     -   (XIV) a polynucleotide that encodes a peptide region of at least         5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,         22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino         acids of a peptide of FIGS. 3A–D in any whole number increment         up to 875 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,         13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,         29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value         greater than 0.5 in the Percent Accessible Residues profile of         FIG. 7;     -   (XV) a polynucleotide that encodes a peptide region of at least         5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,         22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino         acids of a peptide of FIG. 3A–DF in any whole number increment         up to 875 that includes 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12,         13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,         29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value         greater than 0.5 in the Average Flexibility profile of FIG. 8;     -   (XVI) a polynucleotide that encodes a peptide region of at least         5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,         22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino         acids of a peptide of FIGS. 3A–D in any whole number increment         up to 875 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,         13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,         29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value         greater than 0.5 in the Beta-turn profile of FIG. 9;     -   (XVII) a polynucleotide that encodes a peptide region of at         least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,         21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino         acids of a peptide of FIG. 3E in any whole number increment up         to 841 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,         14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,         30, 31, 32, 33, 34, 35 amino acid position(s) having a value         greater than 0.5 in the Hydrophilicity profile of FIG. 5;     -   (XVIII) a polynucleotide that encodes a peptide region of at         least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,         21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino         acids of a peptide of FIG. 3E in any whole number increment up         to 841 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,         14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,         30, 31, 32, 33, 34, 35 amino acid position(s) having a value         less than 0.5 in the Hydropathicity profile of FIG. 6;     -   (XIX) a polynucleotide that encodes a peptide region of at least         5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,         22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino         acids of a peptide of FIG. 3E in any whole number increment up         to 841 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,         14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,         30, 31, 32, 33, 34, 35 amino acid position(s) having a value         greater than 0.5 in the Percent Accessible Residues profile of         FIG. 7;     -   (XX) a polynucleotide that encodes a peptide region of at least         5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,         22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino         acids of a peptide of FIG. 3E in any whole number increment up         to 841 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,         14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,         30, 31, 32, 33, 34, 35 amino acid position(s) having a value         greater than 0.5 in the Average Flexibility profile of FIG. 8;     -   (XXI) a polynucleotide that encodes a peptide region of at least         5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,         22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino         acids of a peptide of FIG. 3E in any whole number increment up         to 841 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,         14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,         30, 31, 32, 33, 34, 35 amino acid position(s) having a value         greater than 0.5 in the Beta-turn profile of FIG. 9

(XXII) a polynucleotide that encodes monocloncal antibody or binding region thereof secreted by a hybridoma entitled X41(3)15 deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, Va. 20110-2209 USA) on Nov. 7, 2002 and assigned as Patent Deposit Designation No. PTA-4791;

(XXIII) a polynucleotide that encodes monocloncal antibody or binding region thereof secreted by a hybridoma entitled X41(3)29 deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, Va. 20110-2209 USA) on Nov. 7, 2002 and assigned as Patent Deposit Designation No. PTA-4791;

(XXIV) a polynucleotide that encodes monocloncal antibody or binding region thereof secreted by a hybridoma entitled X41(3)37 deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, Va. 20110-2209 USA) on Nov. 7, 2002 and assigned as Patent Deposit Designation No. PTA-4791;

(XXV) a polynucleotide that encodes monocloncal antibody or binding region thereof secreted by a hybridoma entitled X41(4)6 deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, Va. 20110-2209 USA) on Nov. 7, 2002 and assigned as Patent Deposit Desianation No. PTA-4794;

(XXVI) a polynucleotide that encodes monocloncal antibody or binding region thereof secreted by a hybridoma entitled X41(3)17 deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, Va. 20110-2209 USA) on Nov. 7, 2002 and assigned as Patent Deposit Designation No. PTA-4792;

(XXVII) a polynucleotide that encodes monocloncal antibody or binding region thereof secreted by a hybridoma entitled X41(3)50 deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, Va. 20110-2209 USA) on Nov. 7, 2002 and assigned as Patent Deposit Designation No. PTA-4793;

-   -   (XXVIII) a polynucleotide that is fully complementary to a         polynucleotide of any one of (I)–(XXVII).     -   (XXIX) a peptide that is encoded by any of (I) to (XXVII); and     -   (XXX) a composition comprising a polynucleotide of any of         (I)–(XXVII) or peptide of (XXIX) together with a pharmaceutical         excipient and/or in a human unit dose form.     -   (XXXI) a method of using a polynucleotide of any (I)–(XXVII) or         peptide of (XXIX) or a composition of (XXX) in a method to         modulate a cell expressing 161P2F10b,     -   (XXXII) a method of using a polynucleotide of any (I)–(XXVII) or         peptide of (XXIX) or a composition of (XXX) in a method to         diagnose, prophylax, prognose, or treat an individual who bears         a cell expressing 161P2F10b     -   (XXXIII) a method of using a polynucleotide of any (I)–(XXVII)         or peptide of (XXIX) or a composition of (XXX) in a method to         diagnose, prophylax, prognose, or treat an individual who bears         a cell expressing 161P2F10b, said cell from a cancer of a tissue         listed in Table I;     -   (XXXIV) a method of using a polynucleotide of any (I)–(XLII) or         peptide of (XXIX) or a composition of (XXX) in a method to         diagnose, prophylax, prognose, or treat a a cancer;     -   (XXXV) a method of using a polynucleotide of any (I)–(XLII) or         peptide of (XXIX) or a composition of (XXX) in a method to         diagnose, prophylax, prognose, or treat a a cancer of a tissue         listed in Table l; and,     -   (XXXVI) a method of using a polynucleotide of any (I)–(XLII) or         peptide of (XXIX) or a composition of (XXX) in a method to         identify or characterize a modulator of a cell expressing         161P2F10b.

As used herein, a range is understood to disclose specifically all whole unit positions thereof.

Typical embodiments of the invention disclosed herein include 161P2F10B polynucleotides that encode specific portions of 161P2F10B mRNA sequences (and those which are complementary to such sequences) such as those that encode the proteins and/or fragments thereof, for example:

(a) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675, 700, 725, 750, 775, 800, 825, 850, 860, 870, 875 or more contiguous amino acids of 161P2F10B variant 1; the maximal lengths relevant for other variants are: variant 2, 875 amino acids; variant 3, 875 amino acids, variant 4, 875 amino acids, and variant 7, 841 amino acids.

For example, representative embodiments of the invention disclosed herein include: polynucleotides and their encoded peptides themselves encoding about amino acid 1 to about amino acid 10 of the 161P2F10B protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 10 to about amino acid 20 of the 161P2F10B protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 20 to about amino acid 30 of the 161P2F10B protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 30 to about amino acid 40 of the 161P2F10B protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 40 to about amino acid 50 of the 161P2F10B protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 50 to about amino acid 60 of the 161P2F10B protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 60 to about amino acid 70 of the 161P2F10B protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 70 to about amino acid 80 of the 161P2F10B protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 80 to about amino acid 90 of the 161P2F10B protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 90 to about amino acid 100 of the 161P2F10B protein shown in FIG. 2 or FIG. 3, in increments of about 10 amino acids, ending at the carboxyl terminal amino acid set forth in FIG. 2 or FIG. 3. Accordingly, polynucleotides encoding portions of the amino acid sequence (of about 10 amino acids), of amino acids, 100 through the carboxyl terminal amino acid of the 161P2F10B protein are embodiments of the invention. Wherein it is understood that each particular amino acid position discloses that position plus or minus five amino acid residues.

Polynucleotides encoding relatively long portions of a 161P2F10B protein are also within the scope of the invention. For example, polynucleotides encoding from about amino acid 1 (or 20 or 30 or 40 etc.) to about amino acid 20, (or 30, or 40 or 50 etc.) of the 161P2F10B protein “or variant” shown in FIG. 2 or FIG. 3 can be generated by a variety of techniques well known in the art. These polynucleotide fragments can include any portion of the 161P2F10B sequence as shown in FIG. 2.

Additional illustrative embodiments of the invention disclosed herein include 161P2F10B polynucleotide fragments encoding one or more of the biological motifs contained within a 161P2F10B protein “or variant sequence”, including one or more of the motif-bearing subsequences of a 161P2F10B protein or variant set forth in Tables VIII–XXI and XXII–XLIX. In another embodiment, typical polynucleotide fragments of the invention encode one or more of the regions of 161P2F10B protein or variant that exhibit homology to a known molecule. In another embodiment of the invention, typical polynucleotide fragments can encode one or more of the 161P2F10B protein or variant N-glycosylation sites, cAMP and cGMP-dependent protein kinase phosphorylation sites, casein kinase II phosphorylation sites or N-myristoylaton site and amidation sites.

Note that to determine the starting position of any peptide set forth in Tables VIII–XXI and Tables XXII to XLIX (collectively HLA Peptide Tables) respective to its parental protein, e.g., variant 1, variant 2, etc., reference is made to three factors: the particular variant, the length of the peptide in an HLA Peptide Table, and the Search Peptides listed in Table LVII. Generally, a unique Search Peptide is used to obtain HLA peptides for a particular variant. The position of each Search Peptide relative to its respective parent molecule is listed in Table VII. Accordingly, if a Search Peptide begins at position “X”, one must add the value “X minus 1” to each position in Tables VIII–XXI and Tables XXII–IL to obtain the actual position of the HLA peptides in their parental molecule. For example 1f a particular Search Peptide begins at position 150 of its parental molecule, one must add 150–1, i.e., 149 to each HLA peptide amino acid position to calculate the position of that amino acid in the parent molecule.

II.A.) Uses of 161P2F10B Polynucleotides

II.A.1.) Monitoring of Genetic Abnormalities

The polynucleotides of the preceding paragraphs have a number of different specific uses. The human 161P2F10B gene maps to the chromosomal location set forth in the Example entitled “Chromosomal Mapping of 161P2F10B.” For example, because the 161P2F10B gene maps to this chromosome, polynucleotides that encode different regions of the 161P2F10B proteins are used to characterize cytogenetic abnormalities of this chromosomal locale, such as abnormalities that are identified as being associated with various cancers. In certain genes, a variety of chromosomal abnormalities including rearrangements have been identified as frequent cytogenetic abnormalities in a number of different cancers (see e g. Krajinovic et al, Mutat. Res. 382(3–4): 81–83 (1998); Johansson et al., Blood 86(10): 3905–3914 (1995) and Finger et al., P.N.A.S. 85(23): 9158–9162 (1988)). Thus, polynucleotides encoding specific regions of the 161P2F10B proteins provide new tools that can be used to delineate, with greater precision than previously possible, cytogenetic abnormalities in the chromosomal region that encodes 161P2F10B that may contribute to the malignant phenotype. In this context, these polynucleotides satisfy a need in the art for expanding the sensitivity of chromosomal screening in order to identify more subtle and less common chromosomal abnormalities (see e.g. Evans et a., Am. J. Obstet. Gynecol 171(4): 1055–1057 (1994)).

Furthermore, as 161P2F10B was shown to be highly expressed in bladder and other cancers, 161P2F10B polynucleotides are used in methods assessing the status of 161P2F10B gene products in normal versus cancerous tissues. Typically, polynucleotides that encode specific regions of the 161P2F10B proteins are used to assess the presence of perturbations (such as deletions, insertions, point mutations, or alterations resulting in a loss of an antigen etc.) in specific regions of the 161P2F10B gene, such as regions containing one or more motifs. Exemplary assays include both RT-PCR assays as well as single-strand conformation polymorphism (SSCP) analysis (see, e.g., Marrogi et al, J. Cutan. Pathol. 26(8): 369–378 (1999), both of which utilize polynucleotides encoding specific regions of a protein to examine these regions within the protein.

II.A.2.) Antisense Embodiments

Other specifically contemplated nucleic acid related embodiments of the invention disclosed herein are genomic DNA, cDNAs, ribozymes, and antisense molecules, as well as nucleic acid molecules based on an alternative backbone, or including alternative bases, whether derived from natural sources or synthesized, and include molecules capable of inhibiting the RNA or protein expression of 161P2F10B. For example, antisense molecules can be RNAs or other molecules, including peptide nucleic acids (PNAs) or non-nucleic acid molecules such as phosphorothioate derivatives that specifically bind DNA or RNA in a base pair-dependent manner. A skilled artisan can readily obtain these classes of nucleic acid molecules using the 161P2F10B polynucleotides and polynucleotide sequences disclosed herein.

Antisense technology entails the administration of exogenous oligonucleotides that bind to a target polynucleotide located within the cells. The term “antisense” refers to the fact that such oligonucleotides are complementary to their intracellular targets, e.g., 161P2F10B. See for example, Jack Cohen, Oligodeoxynucleotides, Antisense Inhibitors of Gene Expression, CRC Press, 1989; and Synthesis 1:1–5 (1988). The 161P2F10B antisense oligonucleotides of the present invention include derivatives such as S-oligonucleotides (phosphorothioate derivatives or S-oligos, see, Jack Cohen, supra), which exhibit enhanced cancer cell growth inhibitory action. S-oligos (nucleoside phosphorothioates) are isoelectronic analogs of an oligonucleotide (O-oligo) in which a nonbridging oxygen atom of the phosphate group is replaced by a sulfur atom. The S-oligos of the present invention can be prepared by treatment of the corresponding O-oligos with 3H-1,2-benzodithiol-3-one-1,1-dioxide, which is a sulfur transfer reagent. See, e.g., lyer, R. P. et al., J. Org. Chem. 55:4693–4698 (1990); and lyer, R. P. et al., J. Am. Chem. Soc. 112:1253–1254(1990). Additional 161P2F10B antisense oligonucleotides of the present invention include morpholino antisense oligonucleotides known in the art (see, e.g., Partridge et al., 1996, Antisense & Nucleic Acid Drug Development 6: 169–175).

The 161P2F10B antisense oligonucleotides of the present invention typically can be RNA or DNA that is complementary to and stably hybridizes with the first 100 5′ codons or last 100 3′ codons of a 161P2F10B genomic sequence or the corresponding mRNA. Absolute complementarity is not required, although high degrees of complementarity are preferred. Use of an oligonucleotide complementary to this region allows for the selective hybridization to 161P2F10B mRNA and not to mRNA specifying other regulatory subunits of protein kinase. In one embodiment, 161P2F10B antisense oligonucleotides of the present invention are 15 to 30-mer fragments of the antisense DNA molecule that have a sequence that hybridizes to 161P2F10B mRNA. Optionally, 161P2F10B antisense oligonucleotide is a 30-mer oligonucleotide that is complementary to a region in the first 10 5′ codons or last 10 3′ codons of 161P2F10B. Alternatively, the antisense molecules are modified to employ ribozymes in the inhibition of 161P2F10B expression, see, e.g., L. A. Couture & D. T. Stinchcomb; Trends Genet 12: 510–515 (1996).

II.A.3.) Primers and Primer Pairs

Further specific embodiments of these nucleotides of the invention include primers and primer pairs, which allow the specific amplification of polynucleotides of the invention or of any specific parts thereof, and probes that selectively or specifically hybridize to nucleic acid molecules of the invention or to any part thereof. Probes can be labeled with a detectable marker, such as, for example, a radioisotope, fluorescent compound, bioluminescent compound, a chemiluminescent compound, metal chelator or enzyme. Such probes and primers are used to detect the presence of a 161P2F10B polynucleotide in a sample and as a means for detecting a cell expressing a 161P2F10B protein.

Examples of such probes include polypeptides comprising all or part of the human 161P2F10B cDNA sequence shown in FIG. 2. Examples of primer pairs capable of specifically amplifying 161P2F10B mRNAs are also described in the Examples. As will be understood by the skilled artisan, a great many different primers and probes can be prepared based on the sequences provided herein and used effectively to amplify and/or detect a 161P2F10B mRNA.

The 161P2F10B polynucleotides of the invention are useful for a variety of purposes, including but not limited to their use as probes and primers for the amplification and/or detection of the 161P2F10B gene(s), mRNA(s), or fragments thereof; as reagents for the diagnosis and/or prognosis of prostate cancer and other cancers; as coding sequences capable of directing the expression of 161P2F10B polypeptides; as tools for modulating or inhibiting the expression of the 161P2F10B gene(s) and/or translation of the 161P2F10B transcript(s); and as therapeutic agents.

The present invention includes the use of any probe as described herein to identify and isolate a 161P2F10B or 161P2F10B related nucleic acid sequence from a naturally occurring source, such as humans or other mammals, as well as the isolated nucleic acid sequence per se, which would comprise all or most of the sequences found in the probe used.

II.A.4.) Isolation of 161P2F10B-Encoding Nucleic Acid Molecules

The 161P2F10B cDNA sequences described herein enable the isolation of other polynucleotides encoding 161P2F10B gene product(s), as well as the isolation of polynucleotides encoding 161P2F10B gene product homologs, alternatively spliced isoforms, allelic variants, and mutant forms of a 161P2F10B gene product as well as polynucleotides that encode analogs of 161P2F10B-related proteins. Various molecular cloning methods that can be employed to isolate full length cDNAs encoding a 161P2F10B gene are well known (see, for example, Sambrook, J. et al, Molecular Cloning: A Laboratory Manual, 2d edition, Cold Spring Harbor Press, New York, 1989; Current Protocols in Molecular Biology. Ausubel et al., Eds., Wiley and Sons, 1995). For example, lambda phage cloning methodologies can be conveniently employed, using commercially available cloning systems (e.g., Lambda ZAP Express, Stratagene). Phage clones containing 161P2F10B gene cDNAs can be identified by probing with a labeled 161P2F10B cDNA or a fragment thereof. For example, in one embodiment, a 161P2F10B cDNA (e.g., FIG. 2) or a portion thereof can be synthesized and used as a probe to retrieve overlapping and full-length cDNAs corresponding to a 161P2F10B gene. A 161P2F10B gene itself can be isolated by screening genomic DNA libraries, bacterial artificial chromosome libraries (BACs), yeast artificial chromosome libraries (YACs), and the like, with 161P2F10B DNA probes or primers.

II.A.5.) Recombinant Nucleic Acid Molecules and Host-Vector Systems

The invention also provides recombinant DNA or RNA molecules containing a 161P2F10B polynucleotide, a fragment, analog or homologue thereof, including but not limited to phages, plasmids, phagemids, cosmids, YACs, BACs, as well as various viral and non-viral vectors well known in the art, and cells transformed or transfected with such recombinant DNA or RNA molecules. Methods for generating such molecules are well known (see, for example, Sambrook et al., 1989, supra).

The invention further provides a host-vector system comprising a recombinant DNA molecule containing a 161P2F10B polynucleotide, fragment, analog or homologue thereof within a suitable prokaryotic or eukaryotichost cell. Examples of suitable eukaryotic host cells include a yeast cell, a plant cell, or an animal cell, such as a mammalian cell or an insect cell (e.g, a baculovirus-infectible cell such as an Sf9 or HighFive cell). Examples of suitable mammalian cells include various prostate cancer cell lines such as DU145 and TsuPrl, other transfectable or transducible prostate cancer cell lines, primary cells (PrEC), as well as a number of mammalian cells routinely used for the expression of recombinant proteins (e.g., COS, CHO, 293, 293T cells). More particularly, a polynucleotide comprising the coding sequence of 161P2F10B or a fragment, analog or homolog thereof can be used to generate 161P2F10B proteins or fragments thereof using any number of host-vector systems routinely used and widely known in the art.

A wide range of host-vector systems suitable for the expression of 161P2F10B proteins or fragments thereof are available, see for example, Sambrook et al., 1989, supra; Current Protocols in Molecular Biology, 1995, supra). Preferred vectors for mammalian expression include but are not limited to pcDNA 3.1 myc-His-tag (Invitrogen) and the retroviral vector pSRαtkneo (Muller et al., 1991, MCB 11:1785). Using these expression vectors, 161P2F10B can be expressed in several prostate cancer and non-prostate cell lines, including for example 293, 293T, rat-1, NIH 3T3 and TsuPr1. The host-vector systems of the invention are useful for the production of a 161P2F10B protein or fragment thereof. Such host-vector systems can be employed to study the functional properties of 161P2F10B and 161P2F108 mutations or analogs.

Recombinant human 161P2F10B protein or an analog or homolog or fragment thereof can be produced by mammalian cells transfected with a construct encoding a 161P2F10B-related nucleotide. For example, 293T cells can be transfected with an expression plasmid encoding 161P2F10B or fragment, analog or homolog thereof, a 161P2F10B-related protein is expressed in the 293T cells, and the recombinant 161P2F10B protein is isolated using standard purification methods (e.g., affinity purification using anti-161P2F10B antibodies). In another embodiment, a 161P2F10B coding sequence is subcloned into the retroviral vector pSRaMSVtkneo and used to infect various mammalian cell lines, such as NIH 3T3, TsuPr1, 293 and rat-1 in order to establish 161P2F10B expressing cell lines. Various other expression systems well known in the art can also be employed. Expression constructs encoding a leader peptide joined in frame to a 161P2F10B coding sequence can be used for the generation of a secreted form of recombinant 161P2F10B protein.

As discussed herein, redundancy in the genetic code permits variation in 161P2F10B gene sequences. In particular, it is known in the art that specific host species often have specific codon preferences, and thus one can adapt the disclosed sequence as preferred for a desired host. For example, preferred analog codon sequences typically have rare codons (i.e., codons having a usage frequency of less than about 20% in known sequences of the desired host) replaced with higher frequency codons. Codon preferences for a specific species are calculated, for example, by utilizing codon usage tables available on the INTERNET such as at URL dna.affrc.go.jp/-nakamura/codon.html.

Additional sequence modifications are known to enhance protein expression in a cellular host. These include elimination of sequences encoding spurious polyadenylation signals, exon/intron splice site signals, transposon-like repeats, and/or other such well-characterized sequences that are deleterious to gene expression. The GC content of the sequence is adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. Where possible, the sequence is modified to avoid predicted hairpin secondary mRNA structures. Other useful modifications include the addition of a translational initiation consensus sequence at the start of the open reading frame, as described in Kozak, Mol. Cell Biol., 9:5073–5080 (1989). Skilled artisans understand that the general rule that eukaryotic ribosomes initiate translation exclusively at the 5′ proximal AUG codon is abrogated only under rare conditions (see, e 9. , Kozak PNAS 92(7): 2662–2666, (1995) and Kozak NAR 15(20): 8125–8148 (1987)).

III.) 161P2F10B-Related Proteins

Another aspect of the present invention provides 161P2F10B-related proteins. Specific embodiments of 161P2F10B proteins comprise a polypeptide having all or part of the amino acid sequence of human 161P2F10B as shown in FIG. 2 or FIG. 3. Alternatively, embodiments of 161P2F10B proteins comprise variant, homolog or analog polypeptides that have alterations in the amino acid sequence of 161P2F10B shown in FIG. 2 or FIG. 3.

Embodiments of a 161P2F10B polypeptide include: a 161P2F10B polypeptide having a sequence shown in FIG. 2, a peptide sequence of a 161P2F10B as shown in FIG. 2 wherein T is U; at least 10 contiguous nucleotides of a polypeptide having the sequence as shown in FIG. 2; or, at least 10 contiguous peptides of a polypeptide having the sequence as shown in FIG. 2 where T is U. For example, embodiments of 161P2F10B peptides comprise, without limitation:

-   -   (I) a protein comprising, consisting essentially of, or         consisting of an amino acid sequence as shown in FIGS. 2A–G or         FIGS. 3A–E;     -   (II) a 161P2F10B-related protein that is at least 90, 91, 92,         93, 94, 95, 96, 97, 98, 99 or 100% homologous to an entire amino         acid sequence shown in FIGS. 2A–G;     -   (III) a 161P2F10B-related protein that is at least 90, 91, 92,         93, 94, 95, 96, 97, 98, 99 or 100% identical to an entire amino         acid sequence shown in FIGS. 2A–G or 3A–E;     -   (IV) a protein that comprises at least one peptide set forth in         Tables VII to XLIX, optionally with a proviso that it is not an         entire protein of FIG. 2;     -   (V) a protein that comprises at least one peptide set forth in         Tables VIII–XXI, collectively, which peptide is also set forth         in Tables XXII to XLIX, collectively, optionally with a proviso         that it is not an entire protein of FIG. 2;     -   (VI) a protein that comprises at least two peptides selected         from the peptides set forth in Tables VIII–XLIX, optionally with         a proviso that it is not an entire protein of FIG. 2;     -   (VII) a protein that comprises at least two peptides selected         from the peptides set forth in Tables VII to XLIX collectively,         with a proviso that the protein is not a contiguous sequence         from an amino acid sequence of FIG. 2;     -   (VIII) a protein that comprises at least one peptide selected         from the peptides set forth in Tables VIII–XXI; and

at least one peptide selected from the peptides set forth in Tables XXII to XLIX, with a proviso that the protein is not a contiguous sequence from an amino acid sequence of FIG. 2;

-   -   (IX) a polypeptide comprising at least 5, 6, 7, 8, 9, 10, 11,         12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,         28, 29, 30, 31, 32, 33, 34, 35 amino acids of a protein of FIG.         3A, 3B, 3C, 3D, or 3E in any whole number increment up to 875,         875, 875, 875, or 841 respectively that includes at least 1, 2,         3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,         21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino         acid position(s) having a value greater than 0.5 in the         Hydrophilicity profile of FIG. 5;     -   (X) a polypeptide comprising at least 5, 6, 7, 8, 9, 10, 11, 12,         13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,         29, 30, 31, 32, 33, 34, 35 amino acids of a protein of FIG. 3A,         3B, 3C, 3D, or 3E in any whole number increment up to 875, 875,         875, 875, or 841 respectively, that includes at least 1, 2, 3,         4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,         21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino         acid position(s) having a value less than 0.5 in the         Hydropathicity profile of FIG. 6;     -   (XI) a polypeptide comprising at least 5, 6, 7, 8, 9, 10, 11,         12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,         28, 29, 30, 31, 32, 33, 34, 35 amino acids of a protein of FIG.         3A, 3B, 3C, 3D, or 3E in any whole number increment up to 875,         875, 875, 875, or 841 respectively, that includes at least 1, 2,         3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,         20,21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35         amino acid position(s) having a value greater than 0.5 in the         Percent Accessible Residues profile of FIG. 7;     -   (XII) a polypeptide comprising at least 5, 6, 7, 8, 9, 10, 11,         12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,         28, 29, 30, 31, 32, 33, 34, 35 amino acids of a protein of FIG.         3A, 3B, 3C, 3D, or 3E in any whole number increment up to 875,         875, 875, 875, or 841 respectively, that includes at least 1, 2,         3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,         21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino         acid position(s) having a value greater than 0.5 in the Average         Flexibility profile of FIG. 8;     -   (XIII) a polypeptide comprising at least 5, 6, 7, 8, 9, 10, 11,         12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,         28, 29, 30, 31, 32, 33, 34, 35 amino acids of a protein of FIG.         3A, 3B, 3C, 3D, or 3E in any whole number increment up to 875,         875, 875, 875, or 841 respectively, that includes at least 1, 2,         3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,         21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino         acid position(s) having a value greater than 0.5 in the         Beta-turn profile of FIG. 9;     -   (XIV) a peptide that occurs at least twice in Tables VIII–XXI         and XXII to XLIX, collectively;     -   (XV) a peptide that occurs at least three times in Tables         VIII–XXI and XXII to XLIX, collectively;     -   (XVI) a peptide that occurs at least four times in Tables         VIII–XXI and XXII to XLIX, collectively;     -   (XVII) a peptide that occurs at least five times in Tables         VIII–XXI and XXII to XLIX, collectively;     -   (XVIII) a peptide that occurs at least once in Tables VIII–XXI,         and at least once in tables XXII to XLIX;     -   (XIX) a peptide that occurs at least once in Tables VIII–XXI,         and at least twice in tables XXII to XLIX;     -   (XX) a peptide that occurs at least twice in Tables VIII–XXI,         and at least once in tables XXII to XLIX;     -   (XXI) a peptide that occurs at least twice in Tables VIII–XXI,         and at least twice in tables XXII to XLIX;     -   (XXII) a peptide which comprises one two, three, four, or five         of the following characteristics, or an oligonucleotide encoding         such peptide:         -   i) a region of at least 5 amino acids of a particular             peptide of FIG. 3, in any whole number increment up to the             full length of that protein in FIG. 3, that includes an             amino acid position having a value equal to or greater than             0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in             the Hydrophilicity profile of FIG. 5;         -   ii) a region of at least 5 amino acids of a particular             peptide of FIG. 3, in any whole number increment up to the             full length of that protein in FIG. 3, that includes an             amino acid position having a value equal to or less than             0.5, 0.4, 0.3, 0.2, 0.1, or having a value equal to 0.0, in             the Hydropathicity profile of FIG. 6;         -   iii) a region of at least 5 amino acids of a particular             peptide of FIG. 3, in any whole number increment up to the             full length of that protein in FIG. 3, that includes an             amino acid position having a value equal to or greater than             0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in             the Percent Accessible Residues profile of FIG. 7;         -   iv) a region of at least 5 amino acids of a particular             peptide of FIG. 3, in any whole number increment up to the             full length of that protein in FIG. 3, that includes an             amino acid position having a value equal to or greater than             0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in             the Average Flexibility profile of FIG. 8; or,         -   v) a region of at least 5 amino acids of a particular             peptide of FIG. 3, in any whole number increment up to the             full length of that protein in FIG. 3, that includes an             amino acid position having a value equal to or greater than             0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in             the Beta-tum profile of FIG. 9;

(XXIII) a monocloncal antibody or binding region thereof secreted by a hybridoma entitled X41(3)15 deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, Va. 20110-2209 USA) on Nov. 7, 2002 and assigned as Patent Deposit Designation No. PTA-4791;

(XXIV) a monocloncal antibody or binding region thereof secreted by a hybridoma entitled X41(3)29 deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, Va. 20110-2209 USA) on Nov. 7, 2002 and assigned as Patent Deposit Designation No. PTA-4791;

(XXV) a monocloncal antibody or binding region thereof secreted by a hybridoma entitled X41(3)37 deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, Va. 20110-2209 USA) on Nov. 7, 2002 and assigned as Patent Deposit Designation No. PTA-4791;

(XXVI) a meneleneal monocloncal antibody or binding region thereof secreted by a hybridoma entitled X41(4)6 deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, Va. 20110-2209 USA) on Nov. 7, 2002 and assigned as Patent Deposit Designation No. PTA-4794;

(XXVII) a monocloncal antibody or binding region thereof secreted by a hybridoma entitled X41(3)17 deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, Va. 20110-2209 USA) on Nov. 7, 2002 and assigned as Patent Deposit Designation No. PTA-4792;

(XXVIII) a monocloncal antibody or binding region thereof secreted by a hybridoma entitled X41(3)50 deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, Va. 20110-2209 USA) on Nov. 7, 2002 and assigned as Patent Deposit Designation No. PTA-4793;

-   -   (XXIX) a composition comprising a peptide of (I)–(XXII) or an         antibody or binding region thereof of (XXIII to XXVIII) together         with a pharmaceutical excipient and/or in a human unit dose         form;     -   (XXX) a method of using a peptide of (I)–(XXII), or an antibody         or binding region thereof of (XXIII to XXVIII) or a composition         of (XXIX) in a method to modulate a cell expressing 161P2F10b,     -   (XXXI) a method of using a peptide of (I)–(XXII) or an antibody         or binding region thereof of (XXIII to XXVIII)or a composition         of (XXIX) in a method to diagnose, prophylax, prognose, or treat         an individual who bears a cell expressing 161P2F10b     -   (XXXII) a method of using a peptide of (I)–(XXII) or an antibody         or binding region thereof of (XXIII to XXVIII) or a         composition (XXIX) in a method to diagnose, prophylax, prognose,         or treat an individual who bears a cell expressing 161P2F10b,         said cell from a cancer of a tissue listed in Table I;     -   (XXXIII) a method of using a peptide of (I)–(XXII) or an         antibody or binding region thereof of (XXIII to XXVIII) or a         composition of (XXIX) in a method to diagnose, prophylax,         prognose, or treat a a cancer;     -   (XXXIV) a method of using a peptide of (I)–(XXII) or an antibody         or binding region thereof of (XXIII to XXVIII) or a composition         of (XXIX) in a method to diagnose, prophylax, prognose, or treat         a a cancer of a tissue listed in Table I; and,     -   (XXXV) a method of using a a peptide of (I)–(XXII) or an         antibody or binding region thereof of (XXIII to XXVIII) or a         composition (XXIX) in a method to identify or characterize a         modulator of a cell expressing 161P2F10b.

As used herein, a range is understood to specifically disclose all whole unit positions thereof.

Typical embodiments of the invention disclosed herein include 161P2F10B polynucleotides that encode specific portions of 161P2F10B mRNA sequences (and those which are complementary to such sequences) such as those that encode the proteins and/or fragments thereof, for example:

(a) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675, 700, 725, 750, 775, 800, 825, 850, 860, 870, 875 or more contiguous amino acids of 161P2F10B variant 1; the maximal lengths relevant for other variants are: variant 2, 875 amino acids; variant 3, 875 amino acids, variant 4, 875, and variant 7, 841 amino acids.

In general, naturally occurring allelic variants of human 161P2F10B share a high degree of structural identity and homology (e.g., 90% or more homology). Typically, alleic variants of a 161P2F10B protein contain conservative amino acid substitutions within the 161P2F10B sequences described herein or contain a substitution of an amino acid from a corresponding position in a homologue of 161P2F10B. One class of 161P2F10B allelic variants are proteins that share a high degree of homology with at least a small region of a particular 161P2F10B amino acid sequence, but further contain a radical departure from the sequence, such as a non-conservative substitution, truncation, insertion or frame shift. In comparisons of protein sequences, the terms, similarity, identity, and homology each have a distinct meaning as appreciated in the field of genetics. Moreover, orthology and paralogy can be important concepts describing the relationship of members of a given protein family in one organism to the members of the same family in other organisms.

Amino acid abbreviations are provided in Table II. Conservative amino acid substitutions can frequently be made in a protein without altering either the conformation or the function of the protein. Proteins of the invention can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 conservative substitutions. Such changes include substituting any of isoleucine (I), valine (V), and leucine (L) for any other of these hydrophobic amino acids; aspartic acid (D) for glutamic acid (E) and vice versa; glutamine (O) for asparagine (N) and vice versa; and serine (S) for threonine (T) and vice versa. Other substitutions can also be considered conservative, depending on the environment of the particular amino acid and its role in the three-dimensional structure of the protein. For example, glycine (G) and alanine (A) can frequently be interchangeable, as can alanine (A) and valine (V). Methionine (M), which is relatively hydrophobic, can frequently be interchanged with leucine and isoleucine, and sometimes with valine. Lysine (K) and arginine (R) are frequently interchangeable in locations in which the significant feature of the amino acid residue is its charge and the differing pK's of these two amino acid residues are not significant. Still other changes can be considered “conservative” in particular environments (see, e.g. Table III herein; pages 13–15 Biochemistry” 2nd ED. Lubert Stryer ed (Stanford University); Henikoff et al., PNAS 1992 Vol 89 10915–10919; Lei et al., J Biol Chem 1995 May 19; 270(20):11882–6).

Embodiments of the invention disclosed herein include a wide variety of art-accepted variants or analogs of 161P2F10B proteins such as polypeptides having amino acid insertions, deletions and substitutions. 161P2F10B variants can be made using methods known in the art such as site-directed mutagenesis, alanine scanning, and PCR mutagenesis. Site-directed mutagenesis (Carter et al, Nucl. Acids Res., 13:4331 (1986); Zoller et al, Nucl. Acids Res., 10:6487 (1987)), cassette mutagenesis (Wells et al., Gene, 34:315 (1985)), restriction selection mutagenesis (Wells et al., Philos. Trans. R. Soc. London SerA, 317:415 (1986)) or other known techniques can be performed on the cloned DNA to produce the 161P2F10B variant DNA.

Scanning amino acid analysis can also be employed to identify one or more amino acids along a contiguous sequence that is involved in a specific biological activity such as a protein-protein interaction. Among the preferred scanning amino acids are relatively small, neutral amino acids. Such amino acids include alanine, glycine, serine, and cysteine. Alanine is typically a preferred scanning amino acid among this group because it eliminates the side-chain beyond the beta-carbon and is less likely to alter the main-chain conformation of the variant. Alanine is also typically preferred because it is the most common amino acid. Further, it is frequently found in both buried and exposed positions (Creighton, The Proteins, (W.H. Freeman & Co., N.Y.); Chothia, J. Mol. Biol., 150:1 (1976)). If alanine substitution does not yield adequate amounts of variant, an isosteric amino acid can be used.

As defined herein, 161P2F10B variants, analogs or homologs, have the distinguishing allribute of having at least one epitope that is “cross reactive” with a 161P2F10B protein having an amino acid sequence of FIG. 3. As used in this sentence, “cross reactive” means that an antibody or T cell that specifically binds to a 161P2F10B variant also specifically binds to a 161P2F10B protein having an amino acid sequence set forth in FIG. 3. A polypeptide ceases to be a variant of a protein shown in FIG. 3, when it no longer contains any epitope capable of being recognized by an antibody or T cell that specifically binds to the starting 161P2F10B protein. Those skilled in the art understand that antbodies that recognize proteins bind to epitopes of varying size, and a grouping of the order of about four or five amino acids, contiguous or not, is regarded as a typical number of amino acids in a minimal epitope. See, e.g., Nair et a., J. Immunol 2000 165(12): 6949–6955; Hebbes et al., Mol Immunol (1989) 26(9):865–73; Schwartz eta!., J Immunol (1985) 135(4):2598–608.

Other classes of 161P2F10B-related protein variants share 70%, 75%, 80%, 85% or 90% or more similarity with an amino acid sequence of FIG. 3, or a fragment thereof. Another specific class of 161P2F10B protein variants or analogs comprises one or more of the 161P2F10B biological motifs described herein or presently known in the art. Thus, encompassed by the present invention are analogs of 161P2F10B fragments (nucleic or amino acid) that have altered functional (e.g. immunogenic) properties relative to the starting fragment. It is to be appreciated that motifs now or which become part of the art are to be applied to the nucleic or amino acid sequences of FIG. 2 or FIG. 3.

As discussed herein, embodiments of the claimed invention include polypeptides containing less than the full amino acid sequence of a 161P2F10B protein shown in FIG. 2 or FIG. 3. For example, representative embodiments of the invention comprise peptides/proteins having any 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more contiguous amino acids of a 161P2F10B protein shown in FIG. 2 or FIG. 3.

Moreover, representative embodiments of the invention disclosed herein include polypeptides consisting of about amino acid 1 to about amino acid 10 of a 161P2F10B protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 10 to about amino acid 20 of a 161P2F10B protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 20 to about amino acid 30 of a 161P2F10B protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 30 to about amino acid 40 of a 161P2F10B protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 40 to about amino acid 50 of a 161P2F10B protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 50 to about amino acid 60 of a 161P2F10B protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 60 to about amino acid 70 of a 161P2F10B protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 70 to about amino acid 80 of a 161P2F10B protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 80 to about amino acid 90 of a 161P2F10B protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 90 to about amino acid 100 of a 161P2F10B protein shown in FIG. 2 or FIG. 3, etc. throughout the entirety of a 161P2F10B amino acid sequence. Moreover, polypeptides consisting of about amino acid 1 (or 20 or 30 or 40 etc.) to about amino acid 20, (or 130, or 140 or 150 etc.) of a 161P2F10B protein shown in FIG. 2 or FIG. 3 are embodiments of the invention. It is to be appreciated that the starting and stopping positions in this paragraph refer to the specified position as well as that position plus or minus 5 residues.

161P2F10B-related proteins are generated using standard peptide synthesis technology or using chemical cleavage methods well known in the art. Alternatively, recombinant methods can be used to generate nucleic acid molecules that encode a 161P2F10B-related protein. In one embodiment, nucleic acid molecules provide a means to generate defined fragments of a 161P2F10B protein (or variants, homologs or analogs thereof).

III.A.) Motif-Bearing Protein Embodiments

Additional illustrative embodiments of the invention disclosed herein include 161P2F10B polypeptides comprising the amino acid residues of one or more of the biological motifs contained within a 161P2F10B polypeptide sequence set forth in FIG. 2 or FIG. 3. Various motifs are known in the art, and a protein can be evaluated for the presence of such motifs by a number of publicly available Internet sites (see, e.g., Epimatrix™ and Epimer™, Brown University, and BIMAS.).

Motif bearing subsequences of all 161P2F10B variant proteins are set forth and identified in Tables VIII–XXI and XXII–XLIX.

Table V sets forth several frequently occurring motifs based on pfam searches (see URL address pfam.wustl.eduI). The columns of Table V list (1) motif name abbreviation, (2) percent identity found amongst the different member of the motif family, (3) motif name or description and (4) most common function; location information is included if the motif is relevant for location.

Polypeptides comprising one or more of the 161P2F10B motifs discussed above are useful in elucidating the specific characteristics of a malignant phenotype in view of the observation that the 161P2F10B motifs discussed above are associated with growth dysregulation and because 161P2F10B is overexpressed in certain cancers (See, e.g., Table I). Casein kinase II, cAMP and camp-dependent protein kinase, and Protein Kinase C, for example, are enzymes known to be associated with the development of the malignant phenotype (see e.g. Chen et al., Lab Invest., 78(2): 165–174 (1998); Gaiddon et al., Endocrinology 136(10): 4331–4338 (1995); Hall et al., Nucleic Acids Research 24(6):1119–1126 (1996); Peterziel et al., Oncogene 18(46): 6322–6329 (1999) and O'Brian, Oncol. Rep. 5(2): 305–309 (1998)). Moreover, both glycosylation and myristoylation are protein modifications also associated with cancer and cancer progression (see e.g. Dennis et al., Biochem. Biophys. Acta 1473(1):21–34 (1999); Raju et al., Exp. Cell Res. 235(1): 145–154 (1997)). Amidation is another protein modification also associated with cancer and cancer progression (see e.g. Treston et al., J. Natl. Cancer Inst. Monogr. (13): 169–175 (1992)).

In another embodiment, proteins of the invention comprise one or more of the immunoreactive epitopes identified in accordance with art-accepted methods, such as the peptides set forth in Tables VIII–XXI and XXII–XLIX. CTL epitopes can be detennined using specific algorithms to identify peptides within a 161P2F10B protein that are capable of optimally binding to specified HLA alleles (e.g., Table IV; Epimatrix™ and Epimer™, Brown University, and BLMAS). Moreover, processes for identifying peptides that have sufficient binding affinity for HLA molecules and which are correlated with being immunogenic epitopes, are well known in the art, and are carried out without undue experimentation. In addition, processes for identifying peptides that are immunogenic epitopes, are well known in the art, and are carried out without undue experimentation either in vitro or in vivo.

Also known in the art are principles for creating analogs of such epitopes in order to modulate immunogenicity. For example, one begins with an epitope that bears a CTL or HTL motif (see, e.g., the HLA Class I and HLA Class II motifs/supermotifs of Table IV). The epitope is analoged by substituting out an amino acid at one of the specified positions, and replacing it with another amino acid specified for that position. For example, on the basis of residues defined in Table IV, one can substitute out a deleterious residue in favor of any other residue, such as a preferred residue; substitute a less-preferred residue with a preferred residue; or substitute an originally-occurring preferred residue with another preferred residue. Substitutions can occur at primary anchor positions or at other positions in a peptide; see, e.g., Table IV.

A variety of references reflect the art regarding the identification and generation of epitopes in a protein of interest as well as analogs thereof. See, for example, WO 97/33602 to Chesnut et al.; Sette, Immunogenetics 1999 50(3–4): 201–212; Sette et al., J. Immunol. 2001 166(2): 1389–1397; Sidney et al., Hum. Immunol. 1997 58(1): 12–20; Kondo et al., Immunogenetics 1997 45(4): 249–258; Sidney et al., J. Immunol. 1996 157(8): 3480–90; and Falk et al., Nature 351: 290–6 (1991); Hunt et al., Science 255:1261–3(1992); Parker et al., J. Immunol. 149:3580–7 (1992); Parker et al., J. Immunol. 152:163–75 (1994)); Kast et al., 1994 152(8): 3904–12; Borras-Cuesta et al., Hum. Immunol. 2000 61(3): 266–278; Alexander et al., J. Immunol. 2000 164(3); 164(3): 1625–1633; Alexander et al., PMID: 7895164, UI: 95202582; O'Sullivan et al., J. Immunol. 1991 147(8): 2663–2669; Alexander et al., Immunity 1994 1(9): 751–761 and Alexander et al., Immunol. Res. 1998 18(2): 79–92.

Related embodiments of the invention include polypeptides comprising combinations of the different motifs set forth in Table VI, and/or, one or more of the predicted CTL epitopes of Tables VIII–XXI and XXII–XLIX, and/or, one or more of the predicted HTL epitopes of Tables XLVI–XLIX, and/or, one or more of the T cell binding motifs known in the art. Preferred embodiments contain no insertions, deletions or substitutions either within the motifs or within the intervening sequences of the polypeptides. In addition, embodiments which include a number of either N-terminal and/or C-terminal amino acid residues on either side of these motifs may be desirable (to, for example, include a greater portion of the polypeptide architecture in which the motif is located). Typically, the number of N-terminal and/or C-terminal amino acid residues on either side of a motif is between about 1 to about 100 amino acid residues, preferably 5 to about 50 amino acid residues.

161P2F10B-related proteins are embodied in many forms, preferably in isolated form. A purified 161P2F10B protein molecule will be substantially free of other proteins or molecules that impair the binding of 161P2F10B to antibody, T cell or other ligand. The nature and degree of isolation and purification will depend on the intended use. Embodiments of a 161P2F10B-related proteins include purified 161P2F10B-related proteins and functional, soluble 161P2F10B-related proteins. In one embodiment, a functional, soluble 161P2F10B protein or fragment thereof retains the ability to be bound by antibody, T cell or other ligand.

The invention also provides 161P2F10B proteins comprising biologically active fragments of a 161P2F10B amino acid sequence shown in FIG. 2 or FIG. 3. Such proteins exhibit properties of the starting 161P2F10B protein, such as the ability to elicit the generation of antibodies that specifically bind an epitope associated with the starting 161P2F10B protein; to be bound by such antibodies; to elicit the activation of HTL or CTL; and/or, to be recognized by HTL or CTL that also specifically bind to the starting protein.

161P2F10B-related polypeptides that contain particularly interesting structures can be predicted and/or identified using various analytical techniques well known in the art, including, for example, the methods of Chou-Fasman, Gamier-Robson, Kyte-Doolittle, Eisenberg, Karplus-Schultz or Jameson-Wolf analysis, or based on immunogenicity. Fragments that contain such structures are particularly useful in generating subunit-specific anti-161P2F10B antibodies or T cells or in identifying cellular factors that bind to 161P2F10B. For example, hydrophilicity profiles can be generated, and immunogenic peptide fragments identified, using the method of Hopp, T. P. and Woods, K. R., 1981, Proc. Natl. Acad. Sci. U.S.A. 78:3824–3828. Hydropathicity profiles can be generated, and immunogenic peptide fragments identified, using the method of Kyte, J. and Doolittle, R. F., 1982, J. Mol. Biol. 157:105–132. Percent (%) Accessible Residues profiles can be generated, and immunogenic peptide fragments identified, using the method of Janin J., 1979, Nature 277:491–492. Average Flexibility profiles can be generated, and immunogenic peptide fragments identified, using the method of Bhaskaran R., Ponnuswamy P. K., 1988, Int. J. Pept. Protein Res. 32:242–255. Beta-turn profiles can be generated, and immunogenic peptide fragments identified, using the method of Deleage, G., Roux B., 1987, Protein Engineering 1:289–294.

CTL epitopes can be determined using specific algorithms to identify peptides within a 161P2F10B protein that are capable of optimally binding to specified HLA alleles (e.g., by using the SYFPEITHI site; the listings in Table IV(A)–(E); Epimatrix™ and Epimer™, Brown University; and BIMAS). Illustrating this, peptide epitopes from 161P2F10B that are presented in the context of human MHC Class I molecules, e.g., HLA-A1, A2, A3, A11, A24, B7 and B35 were predicted (see, e.g., Tables VIII–XXI, XXII–XLIX). Specifically, the complete amino acid sequence of the 161P2F10B protein and relevant portions of other variants, i.e., for HLA Class I predictions 9 flanking residues on either side of a point mutation or exonjuction, and for HLA Class II predictions 14 flanking residues on either side of a point mutation or exon junction corresponding to that variant, were entered into the HLA Peptide Motif Search algorithm found in the Bioinformatics and Molecular Analysis Section (BIMAS) web site listed above; in addition to the site SYFPEITHI.

The HLA peptide motif search algorithm was developed by Dr. Ken Parker based on binding of specific peptide sequences in the groove of HLA Class I molecules, in particular HLA-A2 (see, e.g., Falk et al., Nature 351: 290–6 (1991); Hunt et al., Science 255:1261–3 (1992); Parker et al., J. Immunol. 149:3580–7 (1992); Parker et al., J. Immunol. 152:163–75 (1994)). This algorithm allows location and ranking of 8-mer, 9-mer, and 10-mer peptides from a complete protein sequence for predicted binding to HLA-A2 as well as numerous other HLA Class I molecules. Many HLA class I binding peptides are 8-, 9-, 10 or 11-mers. For example, for Class I HLA-A2, the epitopes preferably contain a leucine (L) or methionine (M) at position 2 and a valine (V) or leucine (L) at the C-terminus (see, e.g., Parker et al., J. Immunol. 149:3580–7 (1992)). Selected results of 161P2F10B predicted binding peptides are shown in Tables VIII–XXI and XXII–XLIX herein. In Tables VIII–XXI and XXII–XLVII, selected candidates, 9-mers and 10-mers, for each family member are shown along with their location, the amino acid sequence of each specific peptide, and an estimated binding score. In Tables XLVI-XLIX, selected candidates, 15-mers, for each family member are shown along with their location, the amino acid sequence of each specific peptide, and an estimated binding score. The binding score corresponds to the estimated half time of dissociation of complexes containing the peptide at 37° C. at pH 6.5. Peptides with the highest binding score are predicted to be the most tightly bound to HLA Class I on the cell surface for the greatest period of time and thus represent the best immunogenic targets for T-cell recognition.

Actual binding of peptides to an HLA allele can be evaluated by stabilization of HLA expression on the antigen-processing defective cell line T2 (see, e.g., Xue et al., Prostate 30:73–8 (1997) and Peshwa et al., Prostate 36:129–38 (1998)). Immunogenicity of specific peptides can be evaluated in vitro by stimulation of CD8+cytotoxic T lymphocytes (CTL) in the presence of antigen presenting cells such as dendritic cells.

It is to be appreciated that every epitope predicted by the BLIMAS site, Epimer™ and Epimatrix™ sites, or specified by the HLA class I or class II motifs available in the art or which become part of the art such as set forth in Table IV (or determined using the SYFPEITHI site or BIMAS are to be “applied” to a 161P2F10B protein in accordance with the invention. As used in this context “applied” means that a 161P2F10B protein is evaluated, e.g., visually or by computer-based patterns finding methods, as appreciated by those of skill in the relevant art. Every subsequence of a 161P2F10B protein of 8, 9, 10, or 11 amino acid residues that bears an HLA Class I motif, or a subsequence of 9 or more amino acid residues that bear an HLA Class II motif are within the scope of the invention.

III.B.) Expression of 161P2F10B-Related Proteins

In an embodiment described in the examples that follow, 161P2F10B can be conveniently expressed in cells (such as 293T cells) transfected with a commercially available expression vector such as a CMV-driven expression vector, encoding 161P2F10B with a C-terminal 6×His and MYC tag (pcDNA3.1/mycHIS, Invitrogen or Tag5, GenHunter Corporation, Nashville Tenn.). The Tag5 vector provides an IgGK secretion signal that can be used to facilitate the production of a secreted 161P2F10B protein in transfected cells. The secreted HIS-tagged 161P2F10B in the culture media can be purified, e.g., using a nickel column using standard techniques.

III.C.) Modifications of 161P2F10B-Related Proteins

Modifications of 161P2F10B-related proteins such as covalent modifications are included within the scope of this invention. One type of covalent modification includes reacting targeted amino acid residues of a 161P2F10B polypeptide with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C-terminal residues of a 161P2F10B protein. Another type of covalent modification of a 161P2F10B polypeptide included within the scope of this invention comprises altering the native glycosylation pattern of a protein of the invention. Another type of covalent modification of 161P2F10B comprises linking a 161P2F10B polypeptide to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol (PEG), polypropylene glycol, or polyoxyalkylenes, in the manner set forth in U.S. Pat. Nos. 4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or 4,179,337.

The 161P2F10B-related proteins of the present invention can also be modified to form a chimeric molecule comprising 161P2F10B fused to another, heterologous polypeptide or amino acid sequence. Such a chimeric molecule can be synthesized chemically or recombinantly. A chimeric molecule can have a protein of the invention fused to another tumor-associated antigen or fragment thereof. Alternatively, a protein in accordance with the invention can comprise a fusion of fragments of a 161P2F10B sequence (amino or nucleic acid) such that a molecule is created that is not, through its length, directly homologous to the amino or nucleic acid sequences shown in FIG. 2 or FIG. 3. Such a chimeric molecule can comprise multiples of the same subsequence of 161P2F10B. A chimeric molecule can comprise a fusion of a 161P2F10B-related protein with a polyhistidine epitope tag, which provides an epitope to which immobilized nickel can selectively bind, with cytokines or with growth factors. The epitope tag is generally placed at the amino- or carboxyl-terminus of a 161P2F10B protein. In an alternative embodiment, the chimeric molecule can comprise a fusion of a 161P2F10B-related protein with an immunoglobulin or a particular region of an immunoglobulin. For a bivalent form of the chimeric molecule (also referred to as an “immunoadhesin”), such a fusion could be to the Fc region of an IgG molecule. The Ig fusions preferably include the substitution of a soluble (transmembrane domain deleted or inactivated) form of a 161P2F10B polypeptide in place of at least one variable region within an Ig molecule. In a preferred embodiment, the immunoglobulin fusion includes the hinge, CH2 and CH3, or the hinge, CH1, CH2 and CH3 regions of an IgG1 molecule. For the production of immunoglobulin fusions see, e.g., U.S. Pat. No. 5,428,130 issued Jun. 27, 1995.

III.D.) Uses of 161P2F10B-related Proteins

The proteins of the invention have a number of different specific uses. As 161P2F10B is highly expressed in prostate and other cancers, 161P2F10B-related proteins are used in methods that assess the status of 161P2F10B gene products in normal versus cancerous tissues, thereby elucidating the malignant phenotype. Typically, polypeptides from specific regions of a 161P2F10B protein are used to assess the presence of perturbations (such as deletions, insertions, point mutations etc.) in those regions (such as regions containing one or more motifs). Exemplary assays utilize antibodies or T cells targeting 161P2F10B-related proteins comprising the amino acid residues of one or more of the biological motifs contained within a 161P2F10B polypeptide sequence in order to evaluate the characteristics of this region in normal versus cancerous tissues or to elicit an immune response to the epitope. Alternatively, 161P2F10B-related proteins that contain the amino acid residues of one or more of the biological motifs in a 161P2F10B protein are used to screen for factors that interact with that region of 161P2F10B.

161P2F10B protein fragments/subsequences are particularly useful in generating and characterizing domain-specific antibodies (e.g, antibodies recognizing an extracellular or intracellular epitope of a 161P2F10B protein), for identifying agents or cellular factors that bind to 161P2F10B or a particular structural domain thereof, and in various therapeutic and diagnostic contexts, including but not limited to diagnostic assays, cancer vaccines and methods of preparing such vaccines.

Proteins encoded by the 161P2F10B genes, or by analogs, homologs or fragments thereof, have a variety of uses, including but not limited to generating antibodies and in methods for identifying ligands and other agents and cellular constituents that bind to a 161P2F10B gene product Antibodies raised against a 161P2F10B protein or fragment thereof are useful in diagnostic and prognostic assays, and imaging methodologies in the management of human cancers characterized by expression of 161P2F10B protein, such as those listed in Table I. Such antibodies can be expressed intracellularly and used in methods of treating patients with such cancers. 161P2F10B-related nucleic acids or proteins are also used in generating HTL or CTL responses.

Various immunological assays useful for the detection of 161P2F10B proteins are used, including but not limited to various types of radioimmunoassays, enzyme-linked immunosorbent assays (ELISA), enzyme-linked immunofluorescent assays (ELIFA), immunocytochemical methods, and the like. Antibodies can be labeled and used as immunological imaging reagents capable of detecting 161P2F10B-expressing cells (e.g., in radioscintigraphic imaging methods). 161P2F10B proteins are also particularly useful in generating cancer vaccines, as further described herein.

IV.) 161P2F10B Antibodies

Another aspect of the invention provides antibodies that bind to 161P2F10B-related proteins. Preferred antibodies specifically bind to a 161P2F10B-related protein and do not bind (or bind weakly) to peptides or proteins that are not 161P2F10B-related proteins. For example, antibodies that bind 161P2F10B can bind 161P2F10B-related proteins such as the homologs or analogs thereof.

161P2F10B antibodies of the invention are particularly useful in cancer (see, e.g., Table I) diagnostic and prognostic assays, and imaging methodologies. Similarly, such antibodies are useful in the treatment, diagnosis, and/or prognosis of other cancers, to the extent 161P2F10B is also expressed or overexpressed in these other cancers. Moreover, intracellularly expressed antibodies (e.g., single chain antibodies) are therapeutically useful in treating cancers in which the expression of 161P2F10B is involved, such as advanced or metastatic prostate cancers.

The invention also provides various immunological assays useful for the detection and quantification of 161P2F10B and mutant 161P2F10B-related proteins. Such assays can comprise one or more 161P2F10B antibodies capable of recognizing and binding a 161P2F10B-related protein, as appropriate. These assays are performed within various immunological assay formats well known in the art, including but not limited to various types of radioimmunoassays, enzyme-linked immunosorbent assays (ELISA), enzyme-linked immunofluorescent assays (ELIFA), and the like.

Immunological non-antibody assays of the invention also comprise T cell immunogenicity assays (inhibitory or stimulatory) as well as major histocompabbility complex (MHC) binding assays.

In addition, immunological imaging methods capable of detecting prostate cancer and other cancers expressing 161P2F10B are also provided by the invention, including but not limited to radioscintgraphic imaging methods using labeled 161P2F10B antibodies. Such assays are clinically useful in the detection, monitoring, and prognosis of 161P2F10B expressing cancers such as prostate cancer.

161P2F10B antibodies are also used in methods for purifying a 161P2F10B-related protein and for isolating 161P2F10B homologues and related molecules. For example, a method of purifying a 161P2F10B-related protein comprises incubating a 161P2F10B antibody, which has been coupled to a solid matrix, with a lysate or other solution containing a 161P2F10B-related protein under conditions that permit the 161P2F10B antibody to bind to the 161P2F10B-related protein; washing the solid matrix to eliminate impurities; and eluting the 161P2F10B-related protein from the coupled antibody. Other uses of 161P2F10B antibodies in accordance with the invention include generating anti-idiotypic antibodies that mimic a 161P2F10B protein.

Various methods for the preparation of antibodies are well known in the art. For example, antibodies can be prepared by immunizing a suitable mammalian host using a 161P2F10B-related protein, peptide, or fragment, in isolated or immunoconjugated form (Antibodies: A Laboratory Manual, CSH Press, Eds., Harlow, and Lane (1988); Harlow, Antibodies, Cold Spring Harbor Press, NY (1989)). In addition, fusion proteins of 161P2F10B can also be used, such as a 161P2F10B GST-fusion protein. In a particular embodiment, a GST fusion protein comprising all or most of the amino acid sequence of FIG. 2 or FIG. 3 is produced, then used as an immunogen to generate appropriate antibodies. In another embodiment, a 161P2F10B-related protein is synthesized and used as an immunogen.

In addition, naked DNA immunization techniques known in the art are used (with or without purified 161P2F10B-related protein or 161P2F10B expressing cells) to generate an immune response to the encoded immunogen (for review, see Donnelly et al, 1997, Ann. Rev. Immunol. 15: 617–648).

The amino acid sequence of a 161P2F10B protein as shown in FIG. 2 or FIG. 3 can be analyzed to select specific regions of the 161P2F10B protein for generating antibodies. For example, hydrophobicity and hydrophilicity analyses of a 161P2F10B amino acid sequence are used to identify hydrophilic regions in the 161P2F10B structure. Regions of a 161P2F10B protein that show immunogenic structure, as well as other regions and domains, can readily be identified using various other methods known in the art, such as Chou-Fasman, Gamier-Robson, Kyte-Doolittle, Eisenberg, Karplus-Schultz or Jameson-Wolf analysis. Hydrophilicity profiles can be generated using the method of Hopp, T. P. and Woods, K. R., 1981, Proc. Natl. Acad. Sci. U.S.A. 78:3824–3828. Hydropathicity profiles can be generated using the method of Kyte, J. and Doolittle, R. F., 1982, J. Mol. Biol. 157:105–132. Percent (%) Accessible Residues profiles can be generated using the method of Janin J., 1979, Nature 277:491–492. Average Flexibility profiles can be generated using the method of Bhaskaran R., Ponnuswamy P. K., 1988, Int. J. Pept. Protein Res. 32:242–255. Beta-turn profiles can be generated using the method of Deleage, G., Roux B., 1987, Protein Engineering 1:289–294. Thus, each region identified by any of these programs or methods is within the scope of the present invention. Methods for the generation of 161P2F10B antibodies are further illustrated by way of the examples provided herein. Methods for preparing a protein or polypeptide for use as an immunogen are well known in the art. Also well known in the art are methods for preparing immunogenic conjugates of a protein with a carrier, such as BSA, KLH or other carrier protein. In some circumstances, direct conjugation using, for example, carbodiimide reagents are used; in other instances linking reagents such as those supplied by Pierce Chemical Co., Rockford, Ill., are effective. Administration of a 161P2F10B immunogen is often conducted by injection over a suitable time period and with use of a suitable adjuvant, as is understood in the art. During the immunization schedule, titers of antibodies can be taken to determine adequacy of antibody formation.

161P2F10B monoclonal antibodies can be produced by various means well known in the art For example, immortalized cell lines that secrete a desired monoclonal antibody are prepared using the standard hybridoma technology of Kohler and Milstein or modifications that immortalize antibody-producing B cells, as is generally known. Immortalized cell lines that secrete the desired antibodies are screened by immunoassay in which the antigen is a 161P2F10B-related protein. When the appropriate immortalized cell culture is identified, the cells can be expanded and antibodies produced either from in vitro cultures or from ascites fluid.

The antibodies or fragments of the invention can also be produced, by recombinant means. Regions that bind specifically to the desired regions of a 161P2F10B protein can also be produced in the context of chimeric or complementarity-determining region (CDR) grafted antbodies of multiple species origin. Humanized or human 161P2F10B antibodies can also be produced, and are preferred for use in therapeutic contexts. Methods for humanizing murine and other non-human antibodies, by substituting one or more of the non-human antibody CDRs for corresponding human antibody sequences, are well known (see for example, Jones et al., 1986, Nature 321: 522–525; Riechmann et al., 1988, Nature 332: 323–327; Verhoeyen et al., 1988, Science 239: 15341536). See also, Carter et a!, 1993, Proc. Natl. Acad. Sci. USA 89: 4285 and Sims et al., 1993, J. Immunol. 151: 2296.

Methods for producing fully human monoclonal antibodies include phage display and transgenic methods (for review, see Vaughan et al., 1998, Nature Biotechnology 16: 535–539). Fully human 161P2F10B monoclonal antibodies can be generated using cloning technologies employing large human 1 g gene combinatorial libraries (i.e., phage display) (Griffiths and Hoogenboom, Building an in vitro immune system: human antibodies from phage display libraries. In: Protein Engineering of Antibody Molecules for Prophylactic and Therapeutic Applications in Man, Clark, M. (Ed.), Nottingham Academic, pp 45–64 (1993); Burton and Barbas, Human Antibodies from combinatorial libraries. Id., pp 65–82). Fully human 161P2F10B monoclonal antibodies can also be produced using transgenic mice engineered to contain human immunoglobulin gene loci as described in PCT Patent Application WO98124893, Kucheriapati and Jakobovits et a!, published Dec. 3, 1997 (see also, Jakobovits, 1998, Exp. Opin. Invest. Drugs 7(4): 607–614; U.S. Pat. Nos. 6,162,963 issued 2000 Dec. 19; U.S. Pat. No. 6,150,584 issued 2000 Nov. 12; and, U.S. Pat. No. 6,114598 issued 2000 Sep. 5). This method avoids the in vitro manipulation required with phage display technology and efficiently produces high affinity authentic human antibodies.

Reactivity of 161P2F10B antibodies with a 161P2F10B-related protein can be established by a number of well known means, including Western blot, immunoprecipitation, ELISA, and FACS analyses using, as appropriate, 161P2F10B-related proteins, 161P2F10B-expressing cells or extracts thereof. A 161P2F10B antibody or fragment thereof can be labeled with a detectable marker or conjugated to a second molecule. Suitable detectable markers include, but are not limited to, a radioisotope, a fluorescent compound, a bioluminescent compound, chemiluminescent compound, a metal chelator or an enzyme. Further, bi-specific antibodies specific for two or more 161P2F10B epitopes are generated using methods generally known in the art. Homodimeric antibodies can also be generated by cross-linking techniques known in the art (e.g., Wolff et al., Cancer Res. 53: 2560–2565).

V.) 161P2F10B Cellular Immune Responses

The mechanism by which T cells recognize antigens has been delineated. Efficacious peptide epitope vaccine compositions of the invention induce a therapeutic or prophylactic immune responses in very broad segments of the world-wide population. For an understanding of the value and efficacy of compositions of the invention that induce cellular immune responses, a brief review of immunology-related technology is provided.

A complex of an HLA molecule and a peptidic antigen acts as the ligand recognized by HLA-restricted T cells (Buus, S. et al., Cell 47:1071, 1986; Babbitt, B. P. et al., Nature 317:359,1985; Townsend, A. and Bodmer, H., Annu. Rev. Immunol. 7:601, 1989; Germain, R. N., Annu. Rev. Immunol. 11:403, 1993). Through the study of single amino acid substituted antigen analogs and the sequencing of endogenously bound, naturally processed peptides, critical residues that correspond to motifs required for specific binding to HLA antigen molecules have been identified and are set forth in Table IV (see also, e.g., Southwood, et al., J. Immunol. 160:3363, 1998; Rammensee, et al., Immunogenetics 41:178, 1995; Rammensee et al., SYFPEITHI, access via World Wide Web at URL (134.2.96.221/scripts.hlaserver.dll/home.htm); Selte, A. and Sidney, J. Curr. Opin. Immunol. 10 478, 1998; Engelhard, V. H., Curr. Opin. Immunol. 6:13, 1994; Sette, A. and Grey, H. M., Curr. Opin. Immunol. 4:79, 1992; Sinigaglia, F. and Hammer, J. Curr. Biol. 6:52, 1994; Ruppert et al., Cell 74:929–937, 1993; Kondo et al., J. Immunol 155:4307–4312, 1995; Sidney et al., J. Immunol. 157:3480–3490, 1996; Sidney et al., Human Immunol. 45:79–93, 1996; Selte, A. and Sidney, J. Immunogenetics 1999 November; 50(3–4):201-12, Review).

Furthermore, x-ray crystallographic analyses of HLA-peptide complexes have revealed pockets within the peptide binding cleftugroove of HLA molecules which accommodate, in an allele-specific mode, residues borne by peptide ligands; these residues in turn determine the HLA binding capacity of the peptides in which they are present. (See, e.g., Madden, D. R. Annu. Rev. Immunol. 13:587, 1995; Smith, et al., Immunity 4:203, 1996; Fremont et al., Immunity 8:305, 1998; Stern et al., Structure 2:245, 1994; Jones, E. Y. Curr. Opin. Immunol. 9:75, 1997; Brown, J. H. et al., Nature 364:33, 1993; Guo, H. C. et al., Proc. Natl. Acad. Sci. USA 90:8053, 1993; Guo, H. C. et al., Nature 360:364, 1992; Silver, M. L. et al., Nature 360:367, 1992; Matsumura, M. et al., Science 257:927, 1992; Madden et al., Cell 70:1035, 1992; Fremont, D. H. et al., Science 257:919, 1992; Saper, M. A., Bjorkman, P. J. and Wiley, D. C., J. Mol. Biol. 219:277, 1991.)

Accordingly, the definition of class I and class II allele-specific HLA binding motifs, or class I or class II supermotifs allows identification of regions within a protein that are correlated with binding to particular HLA antigen(s).

Thus, by a process of HLA motif identification, candidates for epitope-based vaccines have been identified; such candidates can be further evaluated by HLA-peptide binding assays to determine binding affinity and/or the time period of association of the epitope and its corresponding HLA molecule. Additional confirmatory work can be performed to select, amongst these vaccine candidates, epitopes with preferred characteristics in terms of population coverage, and/or immunogenicity.

Various strategies can be utilized to evaluate cellular immunogenicity, including:

1) Evaluation of primary T cell cultures from normal individuals (see, e.g., Wentworth, P. A. et al., Mol. Immunol 32:603, 1995; Celis, E. et al., Proc. Natl. Acad. Sci. USA 91:2105, 1994; Tsai, V. et al., J. Immunol. 158:1796, 1997; Kawashima, I. et al., Human Immunol. 59:1, 1998). This procedure involves the stimulation of peripheral blood lymphocytes (PBL) from normal subjects with a test peptide in the presence of antigen presenting cells in vitro over a period of several weeks. T cells specific for the peptide become activated during this time and are detected using, e.g., a lymphokine- or ⁵¹ Cr-release assay involving peptide sensitized target cells.

2) Immunization of HLA transgenic mice (see, e.g., Wentworth, P. A. et al., J. Immunol. 26:97, 1996; Wentworth, P. A. et al., Int. Immunol. 8:651, 1996; Alexander, J. et al., J. Immunol. 159:4753, 1997). For example, in such methods peptides in incomplete Freund's adjuvant are administered subcutaneously to HLA transgenic mice. Several weeks following immunization, splenocytes are removed and cultured in vitro in the presence of test peptide for approximately one week. Peptide-specific T cells are detected using, e.g., a ⁵¹ Cr-release assay involving peptide sensitized target cells and target cells expressing endogenously generated antigen.

3) Demonstration of recall T cell responses from immune individuals who have been either effectively vaccinated and/or from chronically ill patients (see, e.g., Rehermann, B. et al., J. Exp. Med. 181:1047, 1995; Doolan, D. L. et al., Immunity 7:97, 1997; Bertoni, R. et al., J. Clin. Invest 100:503, 1997; Threlkeld, S. C. et al., J. Immunol. 159:1648, 1997; Diepolder, H. M. et al., J. Virol. 71:6011, 1997). Accordingly, recall responses are detected by culturing PBL from subjects that have been exposed to the antigen due to disease and thus have generated an immune response “naturally”, or from patients who were vaccinated against the antigen. PBL from subjects are cultured in vitro for 1–2 weeks in the presence of test peptide plus antigen presenting cells (APC) to allow activation of “memory” T cells, as compared to “naive” T cells. At the end of the culture period, T cell activity is detected using assays including ⁵¹ Cr release involving peptide-sensitized targets, T cell proliferation, or lymphokine release.

VI.) 161P2F10B Transgenic Animals

Nucleic acids that encode a 161P2F10B-related protein can also be used to generate either transgenic animals or “knock out” animals that, in turn, are useful in the development and screening of therapeutically useful reagents. In accordance with established techniques, cDNA encoding 161P2F10B can be used to clone genomic DNA that encodes 161P2F10B. The cloned genomic sequences can then be used to generate transgenic animals containing cells that express DNA that encode 161P2F10B. Methods for generating transgenic animals, particularly animals such as mice or rats, have become conventional in the art and are described, for example, in U.S. Pat. No. 4,736,866 issued 1998 Apr. 12, and U.S. Pat. No. 4,870,009 issued 1989 Sep. 26. Typically, particular cells would be targeted for 161P2F10B transgene incorporation with tissue-specific enhancers.

Transgenic animals that include a copy of a transgene encoding 161P2F10B can be used to examine the effect of increased expression of DNA that encodes 161P2F10B. Such animals can be used as tester animals for reagents thought to confer protection from, for example, pathological conditions associated with its overexpression. In accordance with this aspect of the invention, an animal is treated with a reagent and a reduced incidence of a pathological condition, compared to untreated animals that bear the transgene, would indicate a potential therapeutic intervention for the pathological condition.

Alternatively, non-human homologues of 161P2F10B can be used to construct a 161P2F10B “knock out” animal that has a defective or altered gene encoding 161P2F10B as a result of homologous recombination between the endogenous gene encoding 161P2F10B and altered genomic DNA encoding 161P2F10B introduced into an embryonic cell of the animal. For example, cDNA that encodes 161P2F10B can be used to clone genomic DNA encoding 161P2F10B in accordance with established techniques. A portion of the genomic DNA encoding 161P2F10B can be deleted or replaced with another gene, such as a gene encoding a selectable marker that can be used to monitor integration. Typically, several kilobases of unaltered flanking DNA (both at the 5′ and 3′ ends) are included in the vector (see, e.g., Thomas and Capecchi, Cell, 51:503 (1987) for a description of homologous recombination vectors). The vector is introduced into an embryonic stem cell line (e.g., by electroporation) and cells in which the introduced DNA has homologously recombined with the endogenous DNA are selected (see, e.g., Li et al., Cell, 69:915 (1992)). The selected cells are then injected into a blastocyst of an animal (e.g., a mouse or rat) to form aggregation chimeras (see, e.g., Bradley, in Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, E. J. Robertson, ed. (IRL, Oxford, 1987), pp. 113–152). A chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal, and the embryo brought to term to create a “knock out” animal. Progeny harboring the homologously recombined DNA in their germ cells can be identified by standard techniques and used to breed animals in which all cells of the animal contain the homologously recombined DNA. Knock out animals can be characterized, for example, for their ability to defend against certain pathological conditions or for their development of pathological conditions due to absence of a 161P2F10B polypeptide.

VII.) Methods for the Detection of 161P2F10B

Another aspect of the present invention relates to methods for detecting 161P2F10B polynucleotides and 161P2F10B-related proteins, as well as methods for identifying a cell that expresses 161P2F10B. The expression profile of 161P2F10B makes it a diagnostic marker for metastasized disease. Accordingly, the status of 161P2F10B gene products provides information useful for predicting a variety of factors including susceptibility to advanced stage disease, rate of progression, and/or tumor aggressiveness. As discussed in detail herein, the status of 161P2F10B gene products in patient samples can be analyzed by a variety protocols that are well known in the art including immunohistochemical analysis, the variety of Northern blotting techniques including in situ hybridization, RT-PCR analysis (for example on laser capture micro-dissected samples), Western blot analysis and tissue array analysis.

More particularly, the invention provides assays for the detection of 161P2F10B polynucleotides in a biological sample, such as serum, bone, prostate, and other tissues, urine, semen, cell preparations, and the like. Detectable 161P2F10B polynucleotides include, for example, a 161P2F10B gene or fragment thereof, 161P2F10B mRNA, alternative splice variant 161P2F10B mRNAs, and recombinant DNA or RNA molecules that contain a 161P2F10B polynucleotide. A number of methods for amplifying and/or detecting the presence of 161P2F10B polynucleotides are well known in the art and can be employed in the practice of this aspect of the invention.

In one embodiment, a method for detecting a 161P2F10B mRNA in a biological sample comprises producing cDNA from the sample by reverse transcription using at least one primer; amplifying the cDNA so produced using a 161P2F10B polynucleotides as sense and antisense primers to amplify 161P2F10B cDNAs therein; and detecting the presence of the amplified 161P2F10B cDNA. Optionally, the sequence of the amplified 161P2F10B cDNA can be determined.

In another embodiment, a method of detecting a 161P2F10B gene in a biological sample comprises first isolating genomic DNA from the sample; amplifying the isolated genomic DNA using 161P2F10B polynucleotides as sense and antisense primers; and detecting the presence of the amplified 161P2F10B gene. Any number of appropriate sense and antisense probe combinations can be designed from a 161P2F10B nucleotide sequence (see, e.g., FIG. 2) and used for this purpose.

The invention also provides assays for detecting the presence of a 161P2F10B protein in a issue or other bioloical sample such as serum, semen, bone, prostate, urine, cell preparations, and the like. Methods for detecting a 161P2F10B-related protein are also well known and include, for example, immunoprecipitation, immunohistochemical analysis, Western blot analysis, molecular binding assays, ELISA, ELIFA and the like. For example, a method of detecting the presence of a 161P2F10B-related protein in a biological sample comprises first contacting the sample with a 161P2F10B antibody, a 161P2F10B-reactive fragment thereof, or a recombinant protein containing an antigen-binding region of a 161P2F10B antibody; and then detecting the binding of 161P2F10B-related protein in the sample.

Methods for identifying a cell that expresses 161P2F10B are also within the scope of the invention. In one embodiment, an assay for identifying a cell that expresses a 161P2F10B gene comprises detecting the presence of 161P2F10B mRNA in the cell. Methods for the detection of particular mRNAs in cells are well known and include, for example, hybridization assays using complementary DNA probes (such as in situ hybridization using labeled 161P2F10B riboprobes, Northern blot and related techniques) and various nucleic acid amplification assays (such as RT-PCR using complementary primers specific for 161P2F10B, and other amplification type detection methods, such as, for example, branched DNA, SISBA, TMA and the like). Alternatively, an assay for identifying a cell that expresses a 161P2F10B gene comprises detecting the presence of 161 F10B-related protein in the cell or secreted by the cell. Various methods for the detection of proteins are well known in the art and are employed for the detection of 161P2F10B-related proteins and cells that express 161P2F10B-related proteins.

161P2F10B expression analysis is also useful as a tool for identifying and evaluating agents that modulate 161P2F10B gene expression. For example, 161P2F10B expression is significantly upregulated in prostate cancer, and is expressed in cancers of the tissues listed in Table I. Identification of a molecule or biological agent that inhibits 161P2F10B expression or over-expression in cancer cells is of therapeutic value. For example, such an agent can be identified by using a screen that quantifies 161P2F10B expression by RT-PCR, nucleic acid hybridization or antibody binding.

VIII.) Methods for Monitoring the Status of 161P2F10B-related Genes and their Products

Oncogenesis is known to be a multistep process where cellular growth becomes progressively dysregulated and cells progress from a normal physiological state to precancerous and then cancerous states (see, e.g., Alers et al., Lab Invest. 77(5): 437–438 (1997) and Isaacs et al., Cancer Surv. 23: 19–32 (1995)). In this context, examining a biological sample for evidence of-dysregulated cell growth (such as aberrant 161P2F10B expression in cancers) allows for early detection of such aberrant physiology, before a pathologic state such as cancer has progressed to a stage that therapeutic options are more limited and or the prognosis is worse. In such examinations, the status of 161P2F10B in a biological sample of interest can be compared, for example, to the status of 161P2F10B in a corresponding normal sample (e.g. a sample from that individual or alternatively another individual that is not affected by a pathology). An alteration in the status of 161P2F10B in the biological sample (as compared to the normal sample) provides evidence of dysregulated cellular growth. In addition to using a biological sample that is not affected by a pathology as a normal sample, one can also use a predetermined normative value such as a predetermined normal level of mRNA expression (see, e.g., Grever et al., J. Comp. Neurol. 1996 Dec. 9; 376(2): 306–14 and U.S. Pat. No. 5,837,501) to compare 161P2F10B status in a sample.

The term “status” in this context is used according to its art accepted meaning and refers to the condition or state of a gene and its products. Typically, skilled artisans use a number of parameters to evaluate the condition or state of a gene and its products. These include, but are not limited to the location of expressed gene products (including the location of 161P2F10B expressing cells) as well as the level, and biological activity of expressed gene products (such as 161P2F10B mRNA, polynucleotides and polypeptides). Typically, an alteration in the status of 161P2F10B comprises a change in the location of 161P2F10B and/or 161P2F10B expressing cells and/or an increase in 161P2F10B mRNA and/or protein expression.

161P2F10B status in a sample can be analyzed by a number of means well known in the art, including without limitation, immunohistochemical analysis, in sdu hybridization, RT-PCR analysis on laser capture micro-dissected samples, Western blot analysis, and tissue array analysis. Typical protocols for evaluating the status of a 161P2F10B gene and gene products are found, for example in Ausubel et al. eds., 1995, Current Protocols In Molecular Biology, Units 2 (Northern Blotting), 4 (Southern Blotting), 15 (Immunoblotting) and 18 (PCR Analysis). Thus, the status of 161P2F10B in a biological sample is evaluated by various methods utilized by skilled artisans including, but not limited to genomic Southern analysis (to examine, for example perturbations in a 161P2F10B gene), Northern analysis and/or PCR analysis of 161P2F10B mRNA (to examine, for example alterations in the polynucleotide sequences or expression levels of 161P2F10B mRNAs), and, Western and/or immunohistochemical analysis (to examine, for example alterations in polypeptide sequences, alterations in polypeptide localization within a sample, alterations in expression levels of 161P2F10B proteins and/or associations of 161P2F10B proteins with polypeptide binding partners). Detectable 161P2F10B polynucleotides include, for example, a 161P2F10B gene or fragment thereof, 161P2F10B mRNA, alternative splice variants, 161P2F10B mRNAs, and recombinant DNA or RNA molecules containing a 161P2F10B polynucleotide.

The expression profile of 161P2F10B makes it a diagnostic marker for local and/or metastasized disease, and provides information on the growth or oncogenic potential of a biological sample. In particular, the status of 161P2F10B provides information useful for predicting susceptibility to particular disease stages, progression, and/or tumor aggressiveness. The invention provides methods and assays for determining 161P2F10B status and diagnosing cancers that express 161P2F10B, such as cancers of the tissues listed in Table I. For example, because 161P2F10B mRNA is so highly expressed in prostate and other cancers relative to normal prostate tissue, assays that evaluate the levels of 161P2F10B mRNA transcripts or proteins in a biological sample can be used to diagnose a disease associated with 161P2F10B dysregulation, and can provide prognostic information useful in defining appropriate therapeutic options.

The expression status of 161P2F10B provides information including the presence, stage and location of dysplastic, precancerous and cancerous cells, predicting susceptibility to various stages of disease, and/or for gauging tumor aggressiveness. Moreover, the expression profile makes it useful as an imaging reagent for metastasized disease. Consequently, an aspect of the invention is directed to the various molecular prognostic and diagnostic methods for examining the status of 161P2F10B in biological samples such as those from individuals suffering from, or suspected of suffering from a pathology characterized by dysregulated cellular growth, such as cancer.

As described above, the status of 161P2F10B in a biological sample can be examined by a number of well-known procedures in the art. For example, the status of 161P2F10B in a biological sample taken from a specific location in the body can be examined by evaluating the sample for the presence or absence of 161P2F10B expressing cells (e.g. those that express 161P2F10B mRNAs or proteins). This examination can provide evidence of dysregulated cellular growth, for example, when 161P2F10B-expressing cells are found in a biological sample that does not normally contain such cells (such as a lymph node), because such alterations in the status of 161P2F10B in a biological sample are often associated with dysregulated cellular growth. Specifically, one indicator of dysregulated cellular growth is the metastases of cancer cells from an organ of origin (such as the prostate) to a different area of the body (such as a lymph node). In this context, evidence of dysregulated cellular growth is important for example because occult lymph node metastases can be detected in a substantial proportion of patients with prostate cancer, and such metastases are associated with known predictors of disease progression (see, e.g., Murphy et al., Prostate 42(4): 315–317 (2000);Su et al., Semin. Surg. Oncol. 18(1): 17–28 (2000) and Freeman et al., J Urol 1995 August 154(2 Pt 1):474–8).

In one aspect, the invention provides methods for monitoring 161P2F10B gene products by determining the status of 161P2F10B gene products expressed by cells from an individual suspected of having a disease associated with dysregulated cell growth (such as hyperplasia or cancer) and then comparing the status so determined to the status of 161P2F10B gene products in a corresponding normal sample. The presence of aberrant 161P2F10B gene products in the test sample relative to the normal sample provides an indication of the presence of dysregulated cell growth within the cells of the individual.

In another aspect, the invention provides assays useful in determining the presence of cancer in an individual, comprising detecting a significant increase in 161P2F10B mRNA or protein expression in a test cell or tissue sample relative to expression levels in the corresponding normal cell or tissue. The presence of 161P2F10B mRNA can, for example, be evaluated in tissues including but not limited to those listed in Table I. The presence of significant 161P2F10B expression in any of these tissues is useful to indicate the emergence, presence and/or severity of a cancer, since the corresponding normal tissues do not express 161P2F10B mRNA or express it at lower levels.

In a related embodiment, 161P2F10B status is determined at the protein level rather than at the nucleic acid level. For example, such a method comprises determining the level of 161P2F10B protein expressed by cells in a test tissue sample and comparing the level so determined to the level of 161P2F10B expressed in a corresponding normal sample. In one embodiment, the presence of 161P2F108 protein is evaluated, for example, using immunohistochemical methods. 161P2F10B antibodies or binding partners capable of detecting 161P2F10B protein expression are used in a variety of assay formats well known in the art for this purpose.

In a further embodiment, one can evaluate the status of 161P2F10B nucleotide and amino acid sequences in a biological sample in order to identify perturbations in the structure of these molecules. These perturbations can include insertions, deletions, substitutions and the like. Such evaluations are useful because perturbations in the nucleotide and amino acid sequences are observed in a large number of proteins associated with a growth dysregulated phenotype (see, e.g., Marrogi et al., 1999, J. Cutan. Pathol. 26(8):369–378). For example, a mutation in the sequence of 161P2F10B may be indicative of the presence or promotion of a tumor. Such assays therefore have diagnostic and predictive value where a mutation in 161P2F10B indicates a potential loss of function or increase in tumor growth.

A wide variety of assays for observing perturbations in nucleotide and amino acid sequences are well known in the art. For example, the size and structure of nucleic acid or amino acid sequences of 161P2F10B gene products are observed by the Northern, Southern, Western, PCR and DNA sequencing protocols discussed herein. In addition, other methods for observing perturbations in nucleotide and amino acid sequences such as single strand conformation polymorphism analysis are well known in the art (see, e.g., U.S. Pat. Nos. 5,382,510 issued 1999 Sep. 7, and U.S. Pat. No. 5,952,170 issued 1995 Jan. 17).

Additionally, one can examine the methylation status of a 161P2F10B gene in a biological sample. Aberrant demethylation and/or hypermethylation of CpG islands in gene 5′ regulatory regions frequently occurs in immortalized and transformed cells, and can result in altered expression of various genes. For example, promoter hypermethylation of the pi-class glutathione S-transferase (a protein expressed in normal prostate but not expressed in >90% of prostate carcinomas) appears to permanently silence transcription of this gene and is the most frequently detected genomic alteration in prostate carcinomas (De Marzo et al., Am. J. Pathol. 155(6): 1985–1992 (1999)). In addition, this alteration is present in at least 70% of cases of high-grade prostatic intraepithelial neoplasia (PIN) (Brooks et al, Cancer Epidemiol. Biomarkers Prev., 1998, 7:531–536). In another example, expression of the LAGE-1 tumor specific gene (which is not expressed in normal prostate but is expressed in 25–50% of prostate cancers) is induced by deoxy-azacytidine in lymphoblastoid cells, suggesting that tumoral expression is due to demethylation (Lethe et al., Int. J. Cancer 76(6): 903–908 (1998)). A variety of assays for examining methylabon status of a gene are well known in the art. For example, one can utilize, in Southern hybridization approaches, methylation-sensitive restriction enzymes that cannot cleave sequences that contain methylated CpG sites to assess the methylabon status of CpG islands. In addition, MSP (methylation specific PCR) can rapidly profile the methylabon status of all the CpG sites present in a CpG island of a given gene. This procedure involves initial modification of DNA by sodium bisulfite (which will convert all unmethylated cytosines to uracil) followed by amplification using primers specific for methylated versus unmethylated DNA. Protocols involving methylation interference can also be found for example in Current Protocols In Molecular Biology, Unit 12, Frederick M. Ausubel et al. eds., 1995.

Gene amplification is an additional method for assessing the status of 161P2F10B. Gene amplification is measured in a sample directly, for example, by conventional Southern blotting or Northern blotting to quantitate the transcription of mRNA (Thomas, 1980, Proc. Natl. Acad. Sci. USA, 77:5201–5205), dot blotting (DNA analysis), or in situ hybridization, using an appropriately labeled probe, based on the sequences provided herein. Alternatively, antibodies are employed that recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. The antibodies in turn are labeled and the assay carried out where the duplex is bound to a surface, so that upon the formation of duplex on the surface, the presence of antibody bound-to the duplex can be detected.

Biopsied tissue or peripheral blood can be conveniently assayed for the presence of cancer cells using for example, Northern, dot blot or RT-PCR analysis to detect 161P2F10B expression. The presence of RT-PCR amplifiable 161P2F10B mRNA provides an indicaton of the presence of cancer. RT-PCR assays are well known in the arL RT-PCR detection assays for tumor cells in peripheral blood are currently being evaluated for use in the diagnosis and management of a number of human solid tumors. In the prostate cancer field, these include RT-PCR assays for the detection of cells expressing PSA and PSM (Verkaik et al., 1997, Urol. Res. 25:373–384; Ghossein et al., 1995, J. Clin. Oncol. 13:1195–2000; Heston et al., 1995, Clin. Chem. 41:1687–1688).

A further aspect of the invention is an assessment of the susceptibility that an individual has for developing cancer. In one embodiment, a method for predicting susceptibility to cancer comprises detecting 161P2F10B mRNA or 161P2F10B protein in a tissue sample, its presence indicating susceptibility to cancer, wherein the degree of 161P2F10B mRNA expression correlates to the degree of susceptibility. In a specific embodiment, the presence of 161P2F10B in prostate or other bssue is examined, with the presence of 161P2F10B in the sample providing an indication of prostate cancer susceptibility (or the emergence or existence of a prostate tumor). Similarly, one can evaluate the integrity 161P2F10B nucleotide and amino acid sequences in a biological sample, in order to identify perturbations in the structure of these molecules such as insertions, deletions, substitutions and the like. The presence of one or more perturbations in 161P2F10B gene products in the sample is an indication of cancer susceptibility (or the emergence or existence of a tumor).

The invention also comprises methods for gauging tumor aggressiveness. In one embodiment, a method for gauging aggressiveness of a tumor comprises determining the level of 161P2F10B mRNA or 161P2F10B protein expressed by tumor cells, comparing the level so determined to the level of 161P2F10B mRNA or 161P2F10B protein expressed in a corresponding normal tissue taken from the same individual or a normal tissue reference sample, wherein the degree of 161P2F10B mRNA or 161P2F10B protein expression in the tumor sample relative to the normal sample indicates the degree of aggressiveness. In a specific embodiment, aggressiveness of a tumor is evaluated by determining the extent to which 161P2F10B is expressed in the tumor cells, with higher expression levels indicating more aggressive tumors. Another embodiment is the evaluation of the integrity of 161P2F10B nucleotide and amino acid sequences in a biological sample, in order to identify perturbations in the structure of these molecules such as insertions, deletions, substitutions and the like. The presence of one or more perturbations indicates more aggressive tumors.

Another embodiment of the invention is directed to methods for observing the progression of a malignancy in an individual over time. In one embodiment, methods for observing the progression of a malignancy in an individual over time comprise determining the level of 161P2F10B mRNA or 161P2F10B protein expressed by cells in a sample of the tumor, comparing the level so determined to the level of 161P2F10B mRNA or 161P2F10B protein expressed in an equivalent issue sample taken from the same individual at a different time, wherein the degree of 161P2F10B mRNA or 161P2F10B protein expression in the tumor sample over time provides information on the progression of the cancer. In a specific embodiment, the progression of a cancer is evaluated by determining 161P2F10B expression in the tumor cells over time, where increased expression over time indicates a progression of the cancer. Also, one can evaluate the integrity 161P2F10B nucleotide and amino acid sequences in a biological sample in order to identify perturbations in the structure of these molecules such as insertions, deletions, substitutions and the like, where the presence of one or more perturbations indicates a progression of the cancer.

The above diagnostic approaches can be combined with any one of a wide variety of prognostic and diagnostic protocols known in the art. For example, another embodiment of the invention is directed to methods for observing a coincidence between the expression of 161P2F10B gene and 161P2F10B gene products (or perturbations in 161P2F10B gene and 161P2F10B gene products) and a factor that is associated with malignancy, as a means for diagnosing and prognosticating the status of a issue sample. A wide variety of factors associated with malignancy can be utilized, such as the expression of genes associated with malignancy (e.g. PSA, PSCA and PSM expression for prostate cancer etc.) as well as gross cytological observations (see, e.g., Bocking et al., 1984, Anal. Quant. Cytol. 6(2):74–88; Epstein, 1995, Hum. Pathol. 26(2):223–9; Thorson et al., 1998, Mod. Pathol. 11 (6):543–51; Baisden et al., 1999, Am. J. Surg. Pathol. 23(8):918–24). Methods for observing a coincidence between the expression of 161P2F10B gene and 161P2F10B gene products (or perturbations in 161P2F10B gene and 161P2F10B gene products) and another factor that is associated with malignancy are useful, for example, because the presence of a set of specific factors that coincide with disease provides information crucial for diagnosing and prognosticating the status of a issue sample.

In one embodiment, methods for observing a coincidence between the expression of 161P2F10B gene and 161P2F10B gene products (or perturbations in 161P2F10B gene and 161P2F10B gene products) and another factor associated with malignancy entails detecting the overexpression of 161P2F10B mRNA or protein in a tissue sample, detecting the overexpression of PSA mRNA or protein in a issue sample (or PSCA or PSM expression), and observing a coincidence of 161P2F10B mRNA or protein and PSA mRNA or protein overexpression (or PSCA or PSM expression). In a specific embodiment, the expression of 161P2F10B and PSA mRNA in prostate bssue is examined, where the coincidence of 161P2F10B and PSA mRNA overexpression in the sample indicates the existence of prostate cancer, prostate cancer susceptibility or the emergence or status of a prostate tumor.

Methods for detecting and quantifying the expression of 161P2F10B mRNA or protein are described herein, and standard nucleic acid and protein detection and quantification technologies are well known in the art. Standard methods for the detection and quantification of 161P2F10B mRNA include in sdu hybridization using labeled 161P2F10B riboprobes, Northern blot and related techniques using 161P2F10B polynucleotide probes, RT-PCR analysis using primers specific for 161P2F10B, and other amplification type detection methods, such as, for example, branched DNA, SISBA, TMA and the like. In a specific embodiment, semi-quantitative RT-PCR is used to detect and quantify 161P2F10B mRNA expression. Any number of primers capable of amplifying 161P2F10B can be used for this purpose, including but not limited to the various primer sets specifically described herein. In a specific embodiment, polyclonal or monoclonal antibodies specifically reactive with the wild-type 161P2F10B protein can be used in an immunohistochemical assay of biopsied tissue.

IX.) Identification of Molecules that Interact with 161P2F10B

The 161P2F10B protein and nucleic acid sequences disclosed herein allow a skilled artisan to identify proteins, small molecules and other agents that interact with 161P2F10B, as well as pathways activated by 161P2F10B via any one of a variety of art accepted protocols. For example, one can utilize one of the so-called interaction trap systems (also referred to as the “two-hybrid assay”). In such systems, molecules interact and reconstitute a transcription factor which directs expression of a reporter gene, whereupon the expression of the reporter gene is assayed. Other systems identify protein-protein interactions in vivo through reconstitution of a eukaryotic transcriptional activator, see, e.g., U.S. Pat. No. 5,955,280 issued 1999 Sep. 21, U.S. Pat. No. 5,925,523 issued 1999 Jul. 20, U.S. Pat. No. 5,846,722 issued 1998 Dec. 8 and U.S. Pat. No. 6,004,746 issued 1999 Dec. 21. Algorithms are also available in the art for genome-based predictions of protein function (see, e.g., Marcole, et al., Nature 402: Nov. 4, 1999, 83–86).

Alternatively one can screen peptide libraries to identify molecules that interact with 161P2F10B protein sequences. In such methods, peptides that bind to 161P2F10B are identified by screening libraries that encode a random or controlled collection of amino acids. Peptides encoded by the libraries are expressed as fusion proteins of bacteriophage coat proteins, the bacteriophage particles are then screened against the 161P2F10B protein(s).

Accordingly, peptides having a wide variety of uses, such as therapeutic, prognostic or diagnostic reagents, are thus identified without any prior information on the structure of the expected ligand or receptor molecule. Typical peptide libraries and screening methods that can be used to identify molecules that interact with 161P2F10B protein sequences are disclosed for example in U.S. Pat. No. 5,723,286 issued 1998 Mar. 3 and U.S. Pat. No. 5,733,731 issued 1998 Mar. 31.

Alternatively, cell lines that express 161P2F10B are used to identify protein-protein interactions mediated by 161P2F10B. Such interactions can be examined using immunoprecipitation techniques (see, e.g., Hamilton B. J., et al. Biochem. Biophys. Res. Commun. 1999, 261:646–51). 161P2F10B protein can be immunoprecipitated from 161P2F10B-expressing cell lines using anti-161P2F10B antibodies. Alternatively, antibodies against His-tag can be used in a cell line engineered to express fusions of 161P2F10B and a His-tag (vectors mentioned above). The immunoprecipitated complex can be examined for protein association by procedures such as Western blotting, ³⁵S-methionine labeling of proteins, protein microsequencing, silver staining and two-dimensional gel electrophoresis.

Small molecules and ligands that interact with 161P2F10B can be identified through related embodiments of such screening assays. For example, small molecules can be identified that interfere with protein function, including molecules that interfere with 161P2F10B's ability to mediate phosphorylation and de-phosphorylation, interaction with DNA or RNA molecules as an indication of regulation of cell cycles, second messenger signaling or tumorigenesis. Similarly, small molecules that modulate 161P2F10B-related ion channel, protein pump, or cell communication functions are identified and used to treat patients that have a cancer that expresses 161P2F10B (see, e.g., Hille, B., Ionic Channels of Excitable Membranes 2^(nd) Ed., Sinauer Assoc., Sunderland, Mass., 1992). Moreover, ligands that regulate 161P2F10B function can be identified based on their ability to bind 161P2F10B and activate a reporter construct. Typical methods are discussed for example in U.S. Pat. No. 5,928,868 issued 1999 Jul. 27, and include methods for forming hybrid ligands in which at least one ligand is a small molecule. In an illustrative embodiment, cells engineered to express a fusion protein of 161P2F10B and a DNA-binding protein are used to co-express a fusion protein of a hybrid ligand/small molecule and a cDNA library transcriptional activator protein. The cells further contain a reporter gene, the expression of which is conditioned on the proximity of the first and second fusion proteins to each other, an event that occurs only if the hybrid ligand binds to target sites on both hybrid proteins. Those cells that express the reporter gene are selected and the unknown small molecule or the unknown ligand is identified. This method provides a means of identifying modulators, which activate or inhibit 161P2F10B.

An embodiment of this invention comprises a method of screening for a molecule that interacts with a 161P2F10B amino acid sequence shown in FIG. 2 or FIG. 3, comprising the steps of contacting a population of molecules with a 161P2F10B amino acid sequence, allowing the population of molecules and the 161P2F10B amino acid sequence to interact under conditions that facilitate an interaction, determining the presence of a molecule that interacts with the 161P2F10B amino acid sequence, and then separating molecules that do not interact with the 161P2F10B amino acid sequence from molecules that do. In a specific embodiment, the method further comprises purifying, characterizing and identifying a molecule that interacts with the 161P2F10B amino acid sequence. The identified molecule can be used to modulate a function performed by 161P2F10B. In a preferred embodiment, the 161P2F10B amino acid sequence is contacted with a library of peptides.

X.) Therapeutic Methods and Compositions

The identification of 161P2F10B as a protein that is normally expressed in a restricted set of tissues, but which is also expressed in prostate and other cancers, opens a number of therapeutic approaches to the treatment of such cancers. As contemplated herein, 161P2F10B functions as a transcription factor involved in activating tumor-promoting genes or repressing genes that block tumorigenesis.

Accordingly, therapeutic approaches that inhibit the activity of a 161P2F10B protein are useful for patients suffering from a cancer that expresses 161P2F10B. These therapeutic approaches generally fall into two classes. One class comprises various methods for inhibiting the binding or association of a 161P2F10B protein with its binding partner or with other proteins. Another class comprises a variety of methods for inhibiting the transcription of a 161P2F10B gene or translation of 161P2F10B mRNA.

X.A.) Anti-Cancer Vaccines

The invention provides cancer vaccines comprising a 161P2F10B-related protein or 161P2F10B-related nucleic acid. In view of the expression of 161P2F10B, cancer vaccines prevent and/or treat 161P2F10B-expressing cancers with minimal or no effects on non-target tissues. The use of a tumor antigen in a vaccine that generates humoral and/or cell-mediated immune responses as ant-cancer therapy is well known in the art and has been employed in prostate cancer using human PSMA and rodent PAP immunogens (Hodge et al., 1995, Int J. Cancer 63:231–237; Fong et al., 1997, J. Immunol. 159:3113–3117).

Such methods can be readily practiced by employing a 161P2F10B-related protein, or a 161P2F10B-encoding nucleic acid molecule and recombinant vectors capable of expressing and presenting the 161P2F10B immunogen (which typically comprises a number of antibody or T cell epitopes). Skilled artisans understand that a wide variety of vaccine systems for delivery of immunoreactive epitopes are known in the art (see, e.g., Heryln et al., Ann Med 1999 February 31(1):66–78; Maruyama et al., Cancer Immunol Immunother 2000 June 49(3):123–32) Briefly, such methods of generating an immune response (e.g. humoral and/or cell-mediated) in a mammal, comprise the steps of: exposing the mammal's immune system to an immunoreactive epitope (e.g. an epitope present in a 161P2F10B protein shown in FIG. 3 or analog or homolog thereof) so that the mammal generates an immune response that is specific for that epitope (e.g. generates antibodies that specifically recognize that epitope). In a preferred method, a 161P2F10B immunogen contains a biological motif, see e.g., Tables VIII–XXI and XXII–XLIX, or a peptide of a size range from 161P2F10B indicated in FIG. 5, FIG. 6, FIG. 7, FIG. 8, and FIG. 9.

The entire 161P2F10B protein, immunogenic regions or epitopes thereof can be combined and delivered by various means. Such vaccine compositions can include, for example, lipopeptides (e.g., Vitiello, A. et al., J. Clin. Invest. 95:341, 1995), peptide compositions encapsulated in poly(DL-lactide-co-glycolide) (“PLG”) microspheres (see, e.g., Eldridge, et al., Molec. Immunol. 28:287–294, 1991: Alonso et al., Vaccine 12:299–306, 1994; Jones et al., Vaccine 13:675–681, 1995), peptide compositions contained in immune stimulating complexes (ISCOMS) (see, e.g., Takahashi et al., Nature 344:873–875, 1990; Hu et al., Clin Exp Immunol. 113:235–243, 1998), multiple antigen peptide systems (MAPs) (see e.g., Tam, J. P., Proc. Natl. Acad. Sci. U.S.A. 85:5409–5413, 1988; Tam, J. P., J. Immunol Methods 196:17–32, 1996), peptides formulated as multivalent peptides; peptides for use in ballistic delivery systems, typically crystallized peptides, viral delivery vectors (Perkus, M. E. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 379, 1996; Chakrabarti, S. et al., Nature 320:535, 1986; Hu, S. L. et al., Nature 320:537,1986; Kieny, M.-P. et al., AIDS Bio/Technology 4:790, 1986; Top, F. H. et al., J. Infect. Dis. 124:148, 1971; Chanda, P. K. et al., Virology 175:535, 1990), particles of viral or synthetic origin (e.g., Kofler, N. et al., J. Immunol. Methods. 192:25,1996; Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993; Falo, L. D., Jr. et al., Nature Med. 7:649,1995), adjuvants (Warren, H. S., Vogel, F. R., and Chedid, L. A. Annu. Rev. Immunol. 4:369, 1986; Gupta, R. K. et al., Vaccine 11:293, 1993), liposomes (Reddy, R. et al., J. Immunol. 148:1585, 1992; Rock, K. L., Immunol. Today 17:131, 1996), or, naked or particle absorbed cDNA (Ulmer, J. B. et al., Science 259:1745, 1993; Robinson, H. L., Hunt, L. A., and Webster, R. G., Vaccine 11:957, 1993; Shiver, J. W. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 423, 1996; Cease, K. B., and Berzofsky, J. A., Annu. Rev. Immunol. 12:923, 1994 and Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993). Toxin-targeted delivery technologies, also known as receptor mediated targeting, such as those of Avant Immunotherapeutics, Inc. (Needham, Mass.) may also be used.

In patients with 161P2F10B-associated cancer, the vaccine compositions of the invention can also be used in conjunction with other treatments used for cancer, e.g., surgery, chemotherapy, drug therapies, radiation therapies, etc. including use in combination with immune adjuvants such as IL-2, IL-12, GM-CSF, and the like.

Cellular Vaccines:

CTL epitopes can be determined using specific algorithms to identify peptides within 161P2F10B protein that bind corresponding HLA alleles (see e.g., Table IV; Epimer™ and Epimatrix™, Brown University; and, BIMAS; and SYFPEITHI). In a preferred embodiment, a 161P2F10B immunogen contains one or more amino acid sequences identified using techniques well known in the art, such as the sequences shown in Tables VIII–XXI and XXII–XLIX or a peptide of 8, 9, 10 or 11 amino acids specified by an HLA Class I motiflsupermotif (e.g., Table IV (A), Table IV (D), or Table IV (E)) and/or a peptide of at least 9 amino acids that comprises an HLA Class II motifYsupermotif (e.g., Table IV (B) or Table IV (C)). As is appreciated in the art, the HLA Class I binding groove is essentially closed ended so that peptides of only a particular size range can fit into the groove and be bound, generally HLA Class I epitopes are 8, 9, 10, or 11 amino acids long. In contrast, the HLA Class II binding groove is essentially open ended; thereforee a peptide of about 9 or more amino acids can be bound by an HLA Class II molecule. Due to the binding groove differences between HLA Class I and II, HLA Class I motifs are length specific, i.e., position two of a Class I motif is the second amino acid in an amino to carboxyl direction of the peptide. The amino acid positions in a Class II motif are relative only to each other, not the overall peptide, i.e., additional amino acids can be attached to the amino and/or carboxyl termini of a motif-bearing sequence. HLA Class II epitopes are often 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 amino acids long, or longer than 25 amino acids.

Antibody-Based Vaccines

A wide variety of methods for generating an immune response in a mammal are known in the art (for example as the first step in the generation of hybridomas). Methods of generating an immune response in a mammal comprise exposing the mammal's immune system to an immunogenic epitope on a protein (e.g. a 161P2F10B protein) so that an immune response is generated. A typical embodiment consists of a method for generating an immune response to 161P2F10B in a host, by contacting the host with a sufficient amount of at least one 161P2F10B B cell orcytotoxic T-cell epitope or analog thereof; and at least one periodic interval thereafter re-contacting the host with the 161P2F10B B cell or cytotoxic T-cell epitope or analog thereof. A specific embodiment consists of a method of generating an immune response against a 161P2F10B-related protein or a man-made multiepitopic peptide comprising: administering 161P2F10B immunogen (e.g. a 161P2F10B protein or a peptide fragment thereof, a 161P2F10B fusion protein or analog etc.) in a vaccine preparation to a human or another mammal. Typically, such vaccine preparations further contain a suitable adjuvant (see, e.g., U.S. Pat. No. 6,146,635) or a universal helper epitope such as a PADRE™ peptide (Epimmune Inc., San Diego, Calif.; see, e.g., Alexander et al., J. Immunol. 2000 164(3); 164(3): 1625–1633; Alexander et al., Immunity 1994 1(9): 751–761 and Alexander et al., Immunol. Res. 1998 18(2): 79–92). An alternative method comprises generating an immune response in an individual against a 161P2F10B immunogen by: administering in vivo to muscle or skin of the individual's body a DNA molecule that comprises a DNA sequence that encodes a 161P2F10B immunogen, the DNA sequence operatively linked to regulatory sequences which control the expression of the DNA sequence; wherein the DNA molecule is taken up by cells, the DNA sequence is expressed in the cells and an immune response is generated against the immunogen (see, e.g., U.S. Pat. No. 5,962,428). Optionally a genetic vaccine facilitator such as anionic lipids; saponins; lectins; estrogenic compounds; hydroxylated lower alkyls; dimethyl sulfoxide; and urea is also administered. In addition, an antiidiotypic antibody can be administered that mimics 161P2F10B, in order to generate a response to the target antigen.

Nucleic Acid Vaccines:

Vaccine compositions of the invention include nucleic acid-mediated modalities. DNA or RNA that encode protein(s) of the invention can be administered to a patient. Genetic immunization methods can be employed to generate prophylactic or therapeutic humoral and cellular immune responses directed against cancer cells expressing 161P2F10B. Constructs comprising DNA encoding a 161P2F10B-related protein/immunogen and appropriate regulatory sequences can be injected directly into muscle or skin of an individual, such that the cells of the muscle or skin take-up the construct and express the encoded 161P2F10B protein immunogen. Alternatively, a vaccine comprises a 161P2F10B-related protein. Expression of the 161P2F10B-related protein immunogen results in the generation of prophylactic or therapeutic humoral and cellular immunity against cells that bear a 161P2F10B protein. Various prophylactic and therapeutic genetic immunization techniques known in the art can be used (for review, see information and references published at Internet address genweb.com). Nucleic acid-based delivery is described, for instance, in Wolff et. al., Science 247:1465 (1990) as well as U.S. Pat. Nos. 5,580,859; 5,589,466; 5,804,566; 5,739,118; 5,736,524; 5,679,647; WO 98/04720. Examples of DNA-based delivery technologies include “naked DNA”, facilitated (bupivicaine, polymers, peptide-mediated) delivery, cationic lipid complexes, and particle-mediated (“gene gun”) or pressure-mediated delivery (see, e.g., U.S. Pat. No. 5,922,687).

For therapeutic or prophylactic immunization purposes, proteins of the invention can be expressed via viral or bacterial vectors. Various viral gene delivery systems that can be used in the practice of the invention include, but are not limited to, vaccinia, fowlpox, canarypox, adenovirus, influenza, poliovirus, adeno-associated virus, lentivinus, and sindbis virus (see, e.g., Restifo, 1996, Curr. Opin. Immunol. 8:658–663; Tsang et at J. Natl. Cancer Inst. 87:982–990 (1995)). Non-viral delivery systems can also be employed by introducing naked DNA encoding a 161P2F10B-related protein into the patient (e.g., intramuscularly or intradermally) to induce an anti-tumor response.

Vaccinia virus is used, for example, as a vector to express nucleotide sequences that encode the peptides of the invention. Upon introduction into a host, the recombinant vaccinia virus expresses the protein immunogenic peptide, and thereby elicits a host immune response. Vaccinia vectors and methods useful in immunization protocols are described in, e.g., U.S. Pat. No. 4,722,848. Another vector is BCG (Bacille Calmette Guerin). BCG vectors are described in Stover et al., Nature 351:456–460 (1991). A wide variety of other vectors useful for therapeutic administration or immunization of the peptides of the invention, e.g. adeno and adeno-associated virus vectors, retroviral vectors, Salmonella typhi vectors, detoxified anthrax toxin vectors, and the like, will be apparent to those skilled in the art from the description herein.

Thus, gene delivery systems are used to deliver a 161P2F10B-related nucleic acid molecule. In one embodiment, the full-length human 161P2F10B cDNA is employed. In another embodiment, 1611P2F10B nucleic acid molecules encoding specific cytotoxic T lymphocyte (CTL) and/or antibody epitopes are employed.

Ex Vivo Vaccines

Various ex vivo strategies can also be employed to generate an immune response. One approach involves the use of antigen presenting cells (APCs) such as dendritic cells (DC) to present 161P2F10B antigen to a patient's immune system. Dendritc cells express MHC class 1 and 11 molecules, B7 co-stimulator, and IL-12, and are thus highly specialized antigen presenting cells. In prostate cancer, autologous dendritic cells pulsed with peptides of the prostate-specific membrane antigen (PSMA) are being used in a Phase I clinical trial to stimulate prostate cancer patients' immune systems (Tjoa et al., 1996, Prostate 28:65–69; Murphy et al., 1996, Prostate 29:371–380). Thus, dendritic cells can be used to present 161P2F10B peptides to T cells in the context of MHC class I or II molecules. In one embodiment, autologous dendritic cells are pulsed with 161P2F10B peptides capable of binding to MHC class I and/or class II molecules. In another embodiment, dendritic cells are pulsed with the complete 161P2F10B protein. Yet another embodiment involves engineering the overexpression of a 161P2F10B gene in dendritic cells using various implementing vectors known in the art, such as adenovirus (Arthur et al., 1997, Cancer Gene Ther. 4:17–25), retrovirus (Henderson et al., 1996, Cancer Res. 56:3763–3770), lentivirus, adeno-associated virus, DNA transfection (Ribas et al., 1997, Cancer Res. 57:2865–2869), or tumor-derived RNA transfection (Ashley et al., 1997, J. Exp. Med. 186:1177–1182). Cells that express 161P2F10B can also be engineered to express immune modulators, such as GM-CSF, and used as immunizing agents.

X.B.) 161P2F10B as a Target for Antibody-Based Therapy

161P2F10B is an attractive target for antibody-based therapeutic strategies. A number of antibody strategies are known in the art for targeting both extracellular and intracellular molecules (see, e.g., complement and ADCC mediated killing as well as the use of intrabodies). Because 161P2F10B is expressed by cancer cells of various lineages relative to corresponding normal cells, systemic administration of 161P2F10B-immunoreactive compositions are prepared that exhibit excellent sensitivity without toxic, non-specific and/or non-target effects caused by binding of the immunoreactive composition to non-target organs and tissues. Antibodies specifically reactive with domains of 161P2F10B are useful to treat 161P2F10B-expressing cancers systemically, either as conjugates with a toxin or therapeutic agent, or as naked antibodies capable of inhibiting cell proliferation or function.

161P2F10B antibodies can be introduced into a patient such that the antibody binds to 161P2F10B and modulates a function, such as an interaction with a binding partner, and consequently mediates destruction of the tumor cells and/or inhibits the growth of the tumor cells. Mechanisms by which such antibodies exert a therapeutic effect can include complement-mediated cytolysis, antibody-dependent cellular cytotoxicity, modulation of the physiological function of 161P2F10B, inhibition of ligand binding or signal transduction pathways, modulation of tumor cell differentiation, alteration of tumor angiogenesis factor profiles, and/or apoptosis.

Those skilled in the art understand that antibodies can be used to specifically target and bind immunogenic molecules such as an immunogenic region of a 161P2F10B sequence shown in FIG. 2 or FIG. 3. In addition, skilled artisans understand that it is routine to conjugate antibodies to cytotoxic agents (see, e.g., Slevers et al. Blood 93:11 3678–3684 (Jun. 1, 1999)). When cytotoxic and/or therapeutic agents are delivered directly to cells, such as by conjugating them to antibodies specific for a molecule expressed by that cell (e.g. 161P2F10B), the cytotoxic agent will exert its known biological effect (i.e. cytotoxicity) on those cells.

A wide variety of compositions and methods for using antibody-cytotoxic agent conjugates to kill cells are known in the art. In the context of cancers, typical methods entail administering to an animal having a tumor a biologically effective amount of a conjugate comprising a selected cytotoxic and/or therapeutic agent linked to a targeting agent (e.g. an anti-161P2F10B antibody) that binds to a marker (e.g. 161P2F10B) expressed, accessible to binding or localized on the cell surfaces. A typical embodiment is a method of delivering a cytotoxic and/or therapeutic agent to a cell expressing 161P2F10B, comprising conjugating the cytotoxic agent to an antibody that immunospecifically binds to a 161P2F10B epitope, and, exposing the cell to the antibody-agent conjugate. Another illustrative embodiment is a method of treating an individual suspected of suffering from metastasized cancer, comprising a step of administering parenterally to said individual a pharmaceutical composition comprising a therapeutically effective amount of an antibody conjugated to a cytotoxic and/or therapeutic agent.

Cancer immunotherapy using anti-161P2F10B antibodies can be done in accordance with various approaches that have been successfully employed in the treatment of other types of cancer, including but not limited to colon cancer (Arlen et al., 1998, Crit. Rev. Immunol. 18:133–138), multiple myeloma (Ozaki et al., 1997, Blood 90:3179–3186, Tsunenari et al., 1997, Blood 90:2437–2444), gastric cancer (Kasprzyk et a., 1992, Cancer Res. 52:2771–2776), B-cell lymphoma (Funakoshi et al., 1996, J. Immunother. Emphasis Tumor Immunol. 19:93–101), leukemia (Zhong et al., 1996, Leuk. Res. 20:581–589), colorectal cancer (Moun et al., 1994, Cancer Res. 54:6160–6166; Velders et al., 1995, Cancer Res. 55:4398–4403), and breast cancer (Shepard et al., 1991, J. Clin. Immunol. 11:117–127). Some therapeutic approaches involve conjugation of naked antibody to a toxin or radioisotope, such as the conjugation of Y⁹¹ or I¹³¹ to anti-CD20 antibodies (e.g., Zevalin™, IDEC Pharmaceuticals Corp. or Bexxar™, Coulter Pharmaceuticals), while others involve co-administration of antibodies and other therapeutic agents, such as Herceptin™ (trastuzumab) with paclitaxel (Genentech, Inc.). The antibodies can be conjugated to a therapeutic agent. To treat prostate cancer, for example, 161P2F10B antibodies can be administered in conjunction with radiation, chemotherapy or hormone ablation. Also, antibodies can be conjugated to a toxin such as calicheamicin (e.g., Mylotarg™, Wyeth-Ayerst, Madison, N.J., a recombinant humanized IgG4 kappa antibody conjugated to antitumor antibiotic calicheamicin) or a maytansinoid (e.g., taxane-based Tumor-Activated Prodrug, TAP, platform, ImmunoGen, Cambridge, Mass., also see e.g., U.S. Pat. No. 5,416,064).

Although 161P2F10B antibody therapy is useful for all stages of cancer, antibody therapy can be particularly appropriate in advanced or metastatic cancers. Treatment with the antibody therapy of the invention is indicated for patients who have received one or more rounds of chemotherapy. Alternatively, antibody therapy of the invention is combined with a chemotherapeutic or radiation regimen for patients who have not received chemotherapeutic treatment. Additionally, antibody therapy can enable the use of reduced dosages of concomitant chemotherapy, particularly for patients who do not tolerate the toxicity of the chemotherapeutic agent very well. Fan et al. (Cancer Res. 53:4637–4642, 1993), Prewett et al. (International J. of Onco. 9:217–224, 1996), and Hancock et al. (Cancer Res. 51:4575–4580, 1991) describe the use of various antibodies together with chemotherapeutic agents.

Although 161P2F10B antibody therapy is useful for all stages of cancer, antibody therapy can be particularly appropriate in advanced or metastatic cancers. Treatment with the antibody therapy of the invention is indicated for patients who have received one or more rounds of chemotherapy. Alternatively, antibody therapy of the invention is combined with a chemotherapeutic or radiation regimen for patients who have not received chemotherapeutic treatment. Additionally, antibody therapy can enable the use of reduced dosages of concomitant chemotherapy, particularly for patients who do not tolerate the toxicity of the chemotherapeutic agent very well.

Cancer patients can be evaluated for the presence and level of 161P2F10B expression, preferably using immunohistochemical assessments of tumor tissue, quantitative 161P2F10B imaging, or other techniques that reliably indicate the presence and degree of 161P2F10B expression. Immunohistochemical analysis of tumor biopsies or surgical specimens is preferred for this purpose. Methods for immunohistochemical analysis of tumor tissues are well known in the art.

Anti-161P2F10B monoclonal antibodies that treat prostate and other cancers include those that initiate a potent immune response against the tumor or those that are directly cytotoxic. In this regard, anti-161P2F10B monoclonal antibodies (mAbs) can elicit tumor cell lysis by either complement-mediated or antibody-dependent cell cytotoxicity (ADCC) mechanisms, both of which require an intact Fc portion of the immunoglobulin molecule for interaction with effector cell Fc receptor sites on complement proteins. In addition, anti-161P2F10B mAbs that exerta direct biological effect on tumor growth are useful to treat cancers that express 161P2F10B. Mechanisms by which directly cytotoxic mAbs act include: inhibition of cell growth, modulation of cellular differentiation, modulation of tumor angiogenesis factor profiles, and the induction of apoptosis. The mechanism(s) by which a particular anti-161P2F10B mAb exerts an anti-tumor effect is evaluated using any number of in vitro assays that evaluate cell death such as ADCC, ADMMC, complement-mediated cell lysis, and so forth, as is generally known in the art.

In some patients, the use of murine or other non-human monoclonal antibodies, or human/mouse chimeric mAbs can induce moderate to strong immune responses against the non-human antibody. This can result in clearance of the antibody from circulation and reduced efficacy. In the most severe cases, such an immune response can lead to the extensive formation of immune complexes which, potentially, can cause renal failure. Accordingly, preferred monoclonal antibodies used in the therapeutic methods of the invention are those that are either fully human or humanized and that bind specifically to the target 161P2F10B antigen with high affinity but exhibit low or no antigenicity in the patient.

Therapeutic methods of the invention contemplate the administration of single anti-161P2F10B mAbs as well as combinations, or cocktails, of different mAbs. Such mAb cocktails can have certain advantages inasmuch as they contain mAbs that target different epitopes, exploit different effector mechanisms or combine directly cytotoxic mAbs with mAbs that rely on immune effector functionality. Such mAbs in combination can exhibit synergistic therapeutic effects. In addition, anti-161P2F10B mAbs can be administered concomitantly with other therapeutic modalities, including but not limited to various chemotherapeutic agents, androgen-blockers, immune modulators (e.g., IL-2, GM-CSF), surgery or radiation. The anti-161P2F10B mAbs are administered in their “naked” or unconjugated form, or can have a therapeutic agent(s) conjugated to them.

Anti-161P2F10B antibody formulations are administered via any route capable of delivering the antibodies to a tumor cell. Routes of administration include, but are not limited to, intravenous, intraperitoneal, intramuscular, intratumor, intradermal, and the like. Treatment generally involves repeated administration of the anti-161P2F10B antibody preparation, via an acceptable route of administration such as intravenous injection (IV), typically at a dose in the range of about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 mg/kg body weight. In general, doses in the range of 10–1000 mg mAb per week are effective and well tolerated.

Based on clinical experience with the Herceptin™ mAb in the treatment of metastatic breast cancer, an initial loading dose of approximately 4 mg/kg patient body weight IV, followed by weekly doses of about 2 mg/kg IV of the anti-161P2F10B mAb preparation represents an acceptable dosing regimen. Preferably, the initial loading dose is administered as a 90-minute or longer infusion. The periodic maintenance dose is administered as a 30 minute or longer infusion, provided the initial dose was well tolerated. As appreciated by those of skill in the art, various factors can influence the ideal dose regimen in a particular case. Such factors include, for example, the binding affinity and half life of the Ab or mAbs used, the degree of 161P2F10B expression in the patient, the extent of circulating shed 161P2F10B antigen, the desired steady-state antibody concentration level, frequency of treatment, and the influence of chemotherapeutic or other agents used in combination with the treatment method of the invention, as well as the health status of a particular patient.

Optionally, patients should be evaluated for the levels of 161P2F10B in a given sample (e.g. the levels of circulating 161P2F10B antigen and/or 161P2F10B expressing cells) in order to assist in the determination of the most effective dosing regimen, etc. Such evaluations are also used for monitoring purposes throughout therapy, and are useful to gauge therapeutic success in combination with the evaluation of other parameters (for example, urine cytology and/or ImmunoCyt levels in bladder cancer therapy, or by analogy, serum PSA levels in prostate cancer therapy).

Anti-idiotypic anti-161P2F10B antibodies can also be used in anti-cancer therapy as a vaccine for inducing an immune response to cells expressing a 161P2F10B-related protein. In particular, the generation of anti-idiotypic antibodies is well known in the art; this methodology can readily be adapted to generate anti-idiotypic anti-161P2F10B antibodies that mimic an epitope on a 161P2F10B-related protein (see, for example, Wagner et al., 1997, Hybridoma 16: 33–40; Foon et al., 1995, J. Clin. Invest. 96:334–342; Herlyn et al., 1996, Cancer Immunol. Immunother. 43:65–76). Such an anti-idiotypic antibody can be used in cancer vaccine strategies.

X.C.) 161P2F10B as a Target for Cellular Immune Responses

Vaccines and methods of preparing vaccines that contain an immunogenically effective amount of one or more HLA-binding peptides as described herein are further embodiments of the invention. Furthermore, vaccines in accordance with the invention encompass compositions of one or more of the claimed peptides. A peptide can be present in a vaccine individually. Alternatively, the peptide can exist as a homopolymer comprising multiple copies of the same peptide, or as a heteropolymer of various peptides. Polymers have the advantage of increased immunological reaction and, where different peptide epitopes are used to make up the polymer, the additional ability to induce antibodies and/or CTLs that react with different antigenic determinants of the pathogenic organism or tumor-related peptide targeted for an immune response. The composition can be a naturally occurring region of an antigen or can be prepared, e.g., recombinantly or by chemical synthesis.

Carriers that can be used with vaccines of the invention are well known in the art, and include, e.g., thyroglobulin, albumins such as human serum albumin, tetanus toxoid, polyamino acids such as poly L-lysine, poly L-glutamic acid, influenza, hepatitis B virus core protein, and the like. The vaccines can contain a physiologically tolerable (i.e., acceptable) diluent such as water, or saline, preferably phosphate buffered saline. The vaccines also typically include an adjuvant. Adjuvants such as incomplete Freund's adjuvant, aluminum phosphate, aluminum hydroxide, or alum are examples of materials well known in the art. Additionally, as disclosed herein, CTL responses can be primed by conjugating peptides of the invention to lipids, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P3CSS). Moreover, an adjuvant such as a synthetic cytosine-phosphorothiolated-guanine-containing (CpG) oligonucleotides has been found to increase CTL responses 10- to 100-fold. (see, e.g. Davila and Celis, J. Immunol. 165:539–547 (2000))

Upon immunization with a peptide composition in accordance with the invention, via injection, aerosol, oral, transdermal, transmucosal, intrapleural, intrathecal, or other suitable routes, the immune system of the host responds to the vaccine by producing large amounts of CTLs and/or HTLs specific for the desired antigen. Consequently, the host becomes at least partially immune to later development of cells that express or overexpress 161P2F10B antigen, or derives at least some therapeutic benefit when the antigen was tumor-associated.

In some embodiments, it may be desirable to combine the class I peptide components with components that induce or facilitate neutralizing antibody and or helper T cell responses directed to the target antigen. A preferred embodiment of such a composition comprises class I and class II epitopes in accordance with the invention. An alternative embodiment of such a composition comprises a class I and/or class II epitope in accordance with the invention, along with a cross reactive HTL epitope such as PADRE™ (Epimmune, San Diego, Calif.) molecule (described e.g., in U.S. Pat. No. 5,736,142).

A vaccine of the invention can also include antigen-presenting cells (APC), such as dendritic cells (DC), as a vehicle to present peptides of the invention. Vaccine compositions can be created in vitro, following dendritic cell mobilization and harvesting, whereby loading of dendritic cells occurs in vitro. For example, dendritic cells are transfected, e.g., with a minigene in accordance with the invention, or are pulsed with peptides. The dendritic cell can then be administered to a patient to elicit immune responses in vivo. Vaccine compositions, either DNA- or peptide-based, can also be administered in vivo in combination with dendritic cell mobilization whereby loading of dendritic cells occurs in vivo.

Preferably, the following principles are utilized when selecting an array of epitopes for inclusion in a polyepitopic composition for use in a vaccine, or for selecting discrete epitopes to be included in a vaccine and/or to be encoded by nucleic acids such as a minigene. It is preferred that each of the following principles be balanced in order to make the selection. The multiple epitopes to be incorporated in a given vaccine composition may be, but need not be, contiguous in sequence in the native antigen from which the epitopes are derived.

1.) Epitopes are selected which, upon administration, mimic immune responses that have been observed to be correlated with tumor clearance. For HLA Class I this includes 3–4 epitopes that come from at least one tumor associated antigen (TM). For HLA Class II a similar rationale is employed; again 3–4 epitopes are selected from at least one TAA (see, e.g., Rosenberg et al., Science 278:1447–1450). Epitopes from one TAA may be used in combination with epitopes from one or more additional TAAs to produce a vaccine that targets tumors with varying expression patterns of frequently-expressed TAAs.

2.) Epitopes are selected that have the requisite binding affinity established to be correlated with immunogenicity: for HLA Class I an IC₅₀ of 500 nM or less, often 200 nM or less; and for Class II an IC₅₀ of 1000 nM or less.

3.) Sufficient supermotif bearing-peptides, or a sufficient array of allele-specific motif-bearing peptides, are selected to give broad population coverage. For example, it is preferable to have at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art, can be employed to assess the breadth, or redundancy of, population coverage.

4.) When selecting epitopes from cancer-related antigens it is often useful to select analogs because the patient may have developed tolerance to the native epitope.

5.) Of particular relevance are epitopes referred to as “nested epitopes.” Nested epitopes occur where at least two epitopes overlap in a given peptide sequence. A nested peptide sequence can comprise B cell, HLA class I and/or HLA class II epitopes. When providing nested epitopes, a general objective is to provide the greatest number of epitopes per sequence. Thus, an aspect is to avoid providing a peptide that is any longer than the amino terminus of the amino terminal epitope and the carboxyl terminus of the carboxyl terminal epitope in the peptide. When providing a multi-epitopic sequence, such as a sequence comprising nested epitopes, it is generally important to screen the sequence in order to insure that it does not have pathological or other deleterious biological properties.

6.) If a polyepitopic protein is created, or when creating a minigene, an objective is to generate the smallest peptide that encompasses the epitopes of interest. This principle is similar, if not the same as that employed when selecting a peptide comprising nested epitopes. However, with an artificial polyepitopic peptide, the size minimization objective is balanced against the need to integrate any spacer sequences between epitopes in the polyepitopic protein. Spacer amino acid residues can, for example, be introduced to avoid junctional epitopes (an epitope recognized by the immune system, not present in the target antigen, and only created by the man-made juxtaposition of epitopes), or to facilitate cleavage between epitopes and thereby enhance epitope presentation. Junctional epitopes are generally to be avoided because the recipient may generate an immune response to that non-native epitope. Of particular concern is a junctional epitope that is a “dominant epitope.” A dominant epitope may lead to such a zealous response that immune responses to other epitopes are diminished or suppressed.

7.) Where the sequences of multiple variants of the same target protein are present, potential peptide epitopes can also be selected on the basis of their conservancy. For example, a criterion for conservancy may define that the entire sequence of an HLA class I binding peptide or the entire 9-mer core of a class II binding peptide be conserved in a designated percentage of the sequences evaluated for a specific protein antigen.

X.C.1. Minigene Vaccines

A number of different approaches are available which allow simultaneous delivery of multiple epitopes. Nucleic acids encoding the peptides of the invention are a particularly useful embodiment of the invention. Epitopes for inclusion in a minigene are preferably selected according to the guidelines set forth in the previous section. A preferred means of administering nucleic acids encoding the peptides of the invention uses minigene constructs encoding a peptide comprising one or multiple epitopes of the invention.

The use of multi-epitope minigenes is described below and in, Ishioka et al., J. Immunol. 162:3915–3925, 1999; An, L. and Whitton, J. L., J. Virol. 71:2292, 1997; Thomson, S. A. et al., J. Immunol. 157:822, 1996; Whitton, J. L. et al., J. Virol. 67:348, 1993; Hanke, R. et al., Vaccine 16:426, 1998. For example, a multi-epitope DNA plasmid encoding supermotif- and/or motif-bearing epitopes derived 161P2F10B, the PADRE®D universal helper T cell epitope or multiple HTL epitopes from 161P2F10B (see e.g., Tables VIII-XXI and XXII to XLIX), and an endoplasmic reticulum-translocating signal sequence can be engineered. A vaccine may also comprise epitopes that are derived from other TAAs.

The immunogenicity of a multi-epitopic minigene can be confirmed in transgenic mice to evaluate the magnitude of CTL induction responses against the epitopes tested. Further, the immunogenicity of DNA-encoded epitopes in vivo can be correlated with the in vitro responses of specific CTL lines against target cells transfected with the DNA plasmid. Thus, these experiments can show that the minigene serves to both: 1.) generate a CTL response and 2.) that the induced CTLs recognized cells expressing the encoded epitopes.

For example, to create a DNA sequence encoding the selected epitopes (minigene) for expression in human cells, the amino acid sequences of the epitopes may be reverse translated. A human codon usage table can be used to guide the codon choice for each amino acid. These epitope-encoding DNA sequences may be directly adjoined, so that when translated, a continuous polypeptide sequence is created. To optimize expression and/or immunogenicity, additional elements can be incorporated into the minigene design. Examples of amino acid sequences that can be reverse translated and included in the minigene sequence include: HLA class I epitopes, HLA class II epitopes, antibody epitopes, a ubiquitination signal sequence, and/or an endoplasmic reticulum targeting signal. In addition, HLA presentation of CTL and HTL epitopes may be improved by including synthetic (e.g. poly-alanine) or naturally-occurring flanking sequences adjacent to the CTL or HTL epitopes; these larger peptides comprising the epitope(s) are within the scope of the invention.

The minigene sequence may be converted to DNA by assembling oligonucleotides that encode the plus and minus strands of the minigene. Overlapping oligonucleotides (30–100 bases long) may be synthesized, phosphorylated, purified and annealed under appropriate conditions using well known techniques. The ends of the oligonucleotides can be joined, for example, using T4 DNA ligase. This synthetic minigene, encoding the epitope polypeptide, can then be cloned into a desired expression vector.

Standard regulatory sequences well known to those of skill in the art are preferably included in the vector to ensure expression in the target cells. Several vector elements are desirable: a promoter with a down-stream cloning site for minigene insertion; a polyadenylation signal for efficient transcription termination; an E. coli origin of replication; and an E. coli selectable marker (e.g. ampicillin or kanamycin resistance). Numerous promoters can be used for this purpose, e.g., the human cytomegalovirus (hCMV) promoter. See, e.g., U.S. Pat. Nos. 5,580,859 and 5,589,466 for other suitable promoter sequences.

Additional vector modifications may be desired to optimize minigene expression and immunogenicity. In some cases, introns are required for efficient gene expression, and one or more synthetic or naturally-occurring introns could be incorporated into the transcribed region of the minigene. The inclusion of mRNA stabilization sequences and sequences for replication in mammalian cells may also be considered for increasing minigene expression.

Once an expression vector is selected, the minigene is cloned into the polylinker region downstream of the promoter. This plasmid is transformed into an appropriate E. coli strain, and DNA is prepared using standard techniques. The orientation and DNA sequence of the minigene, as well as all other elements included in the vector, are confirmed using restriction mapping and DNA sequence analysis. Bacterial cells harboring the correct plasmid can be stored as a master cell bank and a working cell bank.

In addition, immunostimulatory sequences (ISSs or CpGs) appear to play a role in the immunogenicity of DNA vaccines. These sequences may be included in the vector, outside the minigene coding sequence, if desired to enhance immunogenicity.

In some embodiments, a bi-cistronic expression vector which allows production of both the minigene-encoded epitopes and a second protein (included to enhance or decrease immunogenicity) can be used. Examples of proteins or polypeptides that could beneficially enhance the immune response if co-expressed include cytokines (e.g., IL-2, IL-12, GM-CSF), cytokine-inducing molecules (e.g., LeIF), costimulatory molecules, or for HTL responses, pan-DR binding proteins (PADRE™, Epimmune, San Diego, Calif.). Helper (HTL) epitopes can be joined to intracellular targeting signals and expressed separately from expressed CTL epitopes; this allows direction of the HTL epitopes to a cell compartment different than that of the CTL epitopes. If required, this could facilitate more efficient entry of HTL epitopes into the HLA class II pathway, thereby improving HTL induction. In contrast to HTL or CTL induction, specifically decreasing the immune response by co-expression of immunosuppressive molecules (e.g. TGF-β) may be beneficial in certain diseases.

Therapeutic quantities of plasmid DNA can be produced for example, by fermentation in E. coli, followed by purification. Aliquots from the working cell bank are used to inoculate growth medium, and grown to saturation in shaker flasks or a bioreactor according to well-known techniques. Plasmid DNA can be purified using standard bioseparation technologies such as solid phase anion-exchange resins supplied by QIAGEN, Inc. (Valencia, Calif.). If required, supercoiled DNA can be isolated from the open circular and linear forms using gel electrophoresis or other methods.

Purified plasmid DNA can be prepared for injection using a variety of formulations. The simplest of these is reconstitution of lyophilized DNA in sterile phosphate-buffer saline (PBS). This approach, known as “naked DNA,” is currently being used for intramuscular (IM) administration in clinical trials. To maximize the immunotherapeutic effects of minigene DNA vaccines, an alternative method for formulating purified plasmid DNA may be desirable. A variety of methods have been described, and new techniques may become available. Cationic lipids, glycolipids, and fusogenic liposomes can also be used in the formulation (see, e.g., as described by WO 93/24640; Mannino & Gould-Fogerite, BioTechniques 6(7): 682 (1988); U.S. Pat. No. 5,279,833; WO 91/06309; and Felgner, et al., Proc. Nat'l Acad. Sci. USA 84:7413 (1987). In addition, peptides and compounds referred to collectively as protective, interactive, non-condensing compounds (PINC) could also be complexed to purified plasmid DNA to influence variables such as stability, intramuscular dispersion, or trafficking to specific organs or cell types.

Target cell sensitization can be used as a functional assay for expression and HLA class I presentation of minigene-encoded CTL epitopes. For example, the plasmid DNA is introduced into a mammalian cell line that is suitable as a target for standard CTL chromium release assays. The transfection method used will be dependent on the final formulation. Electroporation can be used for “naked” DNA, whereas cationic lipids allow direct in vitro transfection. A plasmid expressing green fluorescent protein (GFP) can be co-transfected to allow enrichment of transfected cells using fluorescence activated cell sorting (FACS). These cells are then chromium-51 (⁵¹Cr) labeled and used as target cells for epitope-specific CTL lines; cytolysis, detected by ⁵¹Cr release, indicates both production of, and HLA presentation of, minigene-encoded CTL epitopes. Expression of HTL epitopes may be evaluated in an analogous manner using assays to assess HTL activity.

In vivo immunogenicity is a second approach for functional testing of minigene DNA formulations. Transgenic mice expressing appropriate human HLA proteins are immunized with the DNA product. The dose and route of administration are formulation dependent (e.g., IM for DNA in PBS, intraperitoneal (i.p.) for lipid-complexed DNA). Twenty-one days after immunization, splenocytes are harvested and restimulated for one week in the presence of peptides encoding each epitope being tested. Thereafter, for CTL effector cells, assays are conducted for cytolysis of peptide-loaded, ⁵¹Cr-labeled target cells using standard techniques. Lysis of target cells that were sensitized by HLA loaded with peptide epitopes, corresponding to minigene-encoded epitopes, demonstrates DNA vaccine function for in vivo induction of CTLs. Immunogenicity of HTL epitopes is confirmed in transgenic mice in an analogous manner.

Alternatively, the nucleic acids can be administered using ballistic delivery as described, for instance, in U.S. Pat. No. 5,204,253. Using this technique, particles comprised solely of DNA are administered. In a further alternative embodiment, DNA can be adhered to particles, such as gold particles.

Minigenes can also be delivered using other bacterial or viral delivery systems well known in the art, e.g., an expression construct encoding epitopes of the invention can be incorporated into a viral vector such as vaccinia.

X.C.2. Combinations of CTL Peptides with Helper Peptides

Vaccine compositions comprising CTL peptides of the invention can be modified, e.g., analoged, to provide desired attributes, such as improved serum half life, broadened population coverage or enhanced immunogenicity.

For instance, the ability of a peptide to induce CTL activity can be enhanced by linking the peptide to a sequence which contains at least one epitope that is capable of inducing a T helper cell response. Although a CTL peptide can be directly linked to a T helper peptide, often CTL epitope/HTL epitope conjugates are linked by a spacer molecule. The spacer is typically comprised of relatively small, neutral molecules, such as amino acids or amino acid mimetics, which are substantially uncharged under physiological conditions. The spacers are typically selected from, e.g., Ala, Gly, or other neutral spacers of nonpolar amino acids or neutral polar amino acids. It will be understood that the optionally present spacer need not be comprised of the same residues and thus may be a hetero- or homo-oligomer. When present, the spacer will usually be at least one or two residues, more usually three to six residues and sometimes 10 or more residues. The CTL peptide epitope can be linked to the T helper peptide epitope either directly or via a spacer either at the amino or carboxy terminus of the CTL peptide. The amino terminus of either the immunogenic peptide or the T helper peptide may be acylated.

In certain embodiments, the T helper peptide is one that is recognized by T helper cells present in a majority of a genetically diverse population. This can be accomplished by selecting peptides that bind to many, most, or all of the HLA class II molecules. Examples of such amino acid bind many HLA Class II molecules include sequences from antigens such as tetanus toxoid at positions 830–843 (QYIKANSKFIGITE; SEQ ID NO: 25), Plasmodium falc:parum circumsporozoite (CS) protein at positions 378–398 (DIEKKIAKMEKASSVFNWNS; SEQ ID NO: 26), and Streptococcus 18 kD protein at positions 116–131 (GAVDSILGGVATYGAA; SEQ ID NO: 27). Other examples include peptides bearing a DR 1-4-7 supermotif, or either of the DR3 motifs.

Alternatively, it is possible to prepare synthetic peptides capable of stimulating T helper lymphocytes, in a loosely HLA-restricted fashion, using amino acid sequences not found in nature (see, e.g., PCT publication WO 95/07707). These synthetic compounds called Pan-DR-binding epitopes (e.g., PADRE™, Epimmune, Inc., San Diego, Calif.) are designed, most preferably, to bind most HLA-DR (human HLA class II) molecules. For instance, a pan-DR-binding epitope peptide having the formula: aKXVAAWTLKAa (SEQ ID NO: 28), where “X” is either cyclohexylalanine, phenylalanine, or tyrosine, and a is either D-alanine or L-alanine, has been found to bind to most HLA-DR alleles, and to stimulate the response of T helper lymphocytes from most individuals, regardless of their HLA type. An alternative of a pan-DR binding epitope comprises all “L” natural amino acids and can be provided in the form of nucleic acids that encode the epitope.

HTL peptide epitopes can also be modified to alter their biological properties. For example, they can be modified to include D-amino acids to increase their resistance to proteases and thus extend their serum half life, or they can be conjugated to other molecules such as lipids, proteins, carbohydrates, and the like to increase their biological activity. For example, a T helper peptide can be conjugated to one or more palmitic acid chains at either the amino or carboxyl termini.

X.C.3. Combinations of CTL Peptides with T Cell Priming Agents

In some embodiments it may be desirable to include in the pharmaceutical compositions of the invention at least one component which primes B lymphocytes or T lymphocytes. Lipids have been identified as agents capable of priming CTL in vivo. For example, palmitic acid residues can be attached to the ε- and α-amino groups of a lysine residue and then linked, e.g., via one or more linking residues such as Gly, Gly-Gly-, Ser, Ser-Ser, or the like, to an immunogenic peptide. The lipidated peptide can then be administered either directly in a micelle or particle, incorporated into a liposome, or emulsified in an adjuvant, e.g., incomplete Freund's adjuvant. In a preferred embodiment, a particularly effective immunogenic composition comprises palmitic acid attached to ε- and α-amino groups of Lys, which is attached via linkage, e.g., Ser-Ser, to the amino terminus of the immunogenic peptide.

As another example of lipid priming of CTL responses, E. coli lipoproteins, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P₃CSS) can be used to prime virus specific CTL when covalently attached to an appropriate peptide (see, e.g., Deres, et al., Nature 342:561, 1989). Peptides of the invention can be coupled to P₃CSS, for example, and the lipopeptide administered to an individual to prime specifically an immune response to the target antigen. Moreover, because the induction of neutralizing antibodies can also be primed with P3CSS-conjugated epitopes, two such compositions can be combined to more effectively elicit both humoral and cell-mediated responses.

X.C.4. Vaccine Compositions Comprising DC Pulsed with CTL and/or HTL Peptides

An embodiment of a vaccine composition in accordance with the invention comprises ex vivo administration of a cocktail of epitope-bearing peptides to PBMC, or isolated DC therefrom, from the patient's blood. A pharmaceutical to facilitate harvesting of DC can be used, such as Progenipoietin™ (Pharmacia-Monsanto, St. Louis, Mo.) or GM-CSFIIL-4. After pulsing the DC with peptides and prior to reinfusion into patients, the DC are washed to remove unbound peptides. In this embodiment, a vaccine comprises peptide-pulsed DCs which present the pulsed peptide epitopes complexed with HLA molecules on their surfaces.

The DC can be pulsed ex vivo with a cocktail of peptides, some of which stimulate CTL responses to 161P2F10B. Optionally, a helper T cell (HTL) peptide, such as a natural or artificial loosely restricted HLA Class II peptide, can be included to facilitate the CTL response. Thus, a vaccine in accordance with the invention is used to treat a cancer which expresses or overexpresses 161P2F10B.

X.D. Adoptive Immunotherapy

Antigenic 161P2F10B-refated peptides are used to elicit a CTL and/or HTL response ex vivo, as well. The resulting CTL or HTL cells, can be used to treat tumors in patients that do not respond to other conventional forms of therapy, or will not respond to a therapeutic vaccine peptide or nucleic acid in accordance with the invention. Ex vivo CTL or HTL responses to a particular antigen are induced by incubating in tissue culture the patient's, or genetically compatible, CTL or HTL precursor cells together with a source of antigen-presenting cells (APC), such as dendritic cells, and the appropriate immunogenic peptide. After an appropriate incubation time (typically about 7–28 days), in which the precursor cells are activated and expanded into effector cells, the cells are infused back into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cell (e.g., a tumor cell). Transfected dendritic cells may also be used as antigen presenting cells.

X.E. Administration of Vaccines for Therapeutic or Prophylactic Purposes

Pharmaceutical and vaccine compositions of the invention are typically used to treat and/or prevent a cancer that expresses or overexpresses 161P2F10B. In therapeutic applications, peptide and/or nucleic acid compositions are administered to a patient in an amount sufficient to elicit an effective B cell, CTL and/or HTL response to the antigen and to cure or at least partially arrest or slow symptoms and/or complications. An amount adequate to accomplish this is defined as “therapeutically effective dose.” Amounts effective for this use will depend on, e.g., the particular composition administered, the manner of administration, the stage and severity of the disease being treated, the weight and general state of health of the patient, and the judgment of the prescribing physician.

For pharmaceutical compositions, the immunogenic peptides of the invention, or DNA encoding them, are generally administered to an individual already bearing a tumor that expresses 161P2F10B. The peptides or DNA encoding them can be administered individually or as fusions of one or more peptide sequences. Patients can be treated with the immunogenic peptides separately or in conjunction with other treatments, such as surgery, as appropriate.

For therapeutic use, administration should generally begin at the first diagnosis of 161P2F10B-associated cancer. This is followed by boosting doses until at least symptoms are substantially abated and for a period thereafter. The embodiment of the vaccine composition (i.e., including, but not limited to embodiments such as peptide cocktails, polyepitopic polypeptides, minigenes, or TAA-specific CTLs or pulsed dendritic cells) delivered to the patient may vary according to the stage of the disease or the patient's health status. For example, in a patient with a tumor that expresses 161P2F10B, a vaccine comprising 161P2F10B-specific CTL may be more efficacious in killing tumor cells in patient with advanced disease than alternative embodiments.

It is generally important to provide an amount of the peptide epitope delivered by a mode of administration sufficient to stimulate effectively a cytotoxic T cell response; compositions which stimulate helper T cell responses can also be given in accordance with this embodiment of the invention.

The dosage for an initial therapeutic immunization generally occurs in a unit dosage range where the lower value is about 1, 5, 50, 500, or 1,000 μg and the higher value is about 10,000; 20,000; 30,000; or 50,000 μg. Dosage values for a human typically range from about 500 μg to about 50,000 μg per 70 kilogram patient. Boosting dosages of between about 1.0 μg to about 50,000 μg of peptide pursuant to a boosting regimen over weeks to months may be administered depending upon the patient's response and condition as determined by measuring the specific activity of CTL and HTL obtained from the patient's blood. Administration should continue until at least clinical symptoms or laboratory tests indicate that the neoplasia, has been eliminated or reduced and for a period thereafter. The dosages, routes of administration, and dose schedules are adjusted in accordance with methodologies known in the art.

In certain embodiments, the peptides and compositions of the present invention are employed in serious disease states, that is, life-threatening or potentially life threatening situations. In such cases, as a result of the minimal amounts of extraneous substances and the relative nontoxic nature of the peptides in preferred compositions of the invention, it is possible and may be felt desirable by the treating physician to administer substantial excesses of these peptide compositions relative to these stated dosage amounts.

The vaccine compositions of the invention can also be used purely as prophylactic agents. Generally the dosage for an initial prophylactic immunization generally occurs in a unit dosage range where the lower value is about 1, 5, 50, 500, or 1000 μg and the higher value is about 10,000; 20,000; 30,000; or 50,000 μg. Dosage values for a human typically range from about 500 μg to about 50,000 μg per 70 kilogram patient. This is followed by boosting dosages of between about 1.0 μg to about 50,000 μg of peptide administered at defined intervals from about four weeks to six months after the initial administration of vaccine. The immunogenicity of the vaccine can be assessed by measuring the specific activity of CTL and HTL obtained from a sample of the patient's blood.

The pharmaceutical compositions for therapeutic treatment are intended for parenteral, topical, oral, nasal, intrathecal, or local (e.g. as a cream or topical ointment) administration. Preferably, the pharmaceutical compositions are administered parentally, e.g., intravenously, subcutaneously, intradermally, or intramuscularly. Thus, the invention provides compositions for parenteral administration which comprise a solution of the immunogenic peptides dissolved or suspended in an acceptable carrier, preferably an aqueous carrier.

A variety of aqueous carriers may be used, e.g., water, buffered water, 0.8% saline, 0.3% glycine, hyaluronic acid and the like. These compositions may be sterilized by conventional, well-known sterilization techniques, or may be sterile filtered. The resulting aqueous solutions may be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration.

The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH-adjusting and buffering agents, tonicity adjusting agents, wetting agents, preservatives, and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc.

The concentration of peptides of the invention in the pharmaceutical formulations can vary widely, i.e., from less than about 0.1%, usually at or at least about 2% to as much as 20% to 50% or more by weight, and will be selected primarily by fluid volumes, viscosities, etc., in accordance with the particular mode of administration selected.

A human unit dose form of a composition is typically included in a pharmaceutical composition that comprises a human unit dose of an acceptable carrier, in one embodiment an aqueous carrier, and is administered in a volume/quantity that is known by those of skill in the art to be used for administration of such compositions to humans (see, e.g., Remington's Pharmaceutical Sciences, 17^(th) Edition, A. Gennaro, Editor, Mack Publishing Co., Easton, Pa., 1985). For example a peptide dose for initial immunization can be from about 1 to about 50,000 μg, generally 100–5,000 μg, for a 70 kg patient. For example, for nucleic acids an initial immunization may be performed using an expression vector in the form of naked nucleic acid administered IM (or SC or ID) in the amounts of 0.55 mg at multiple sites. The nucleic acid (0.1 to 1000 μg) can also be administered using a gene gun. Following an incubation period of 3–4 weeks, a booster dose is then administered. The booster can be recombinant fowlpox virus administered at a dose of 5–10⁷ to 5×10⁹ pfu.

For antibodies, a treatment generally involves repeated administration of the anti-161 P2F10B antibody preparation, via an acceptable route of administration such as intravenous injection (IV), typically at a dose in the range of about 0.1 to about 10 mg/kg body weight. In general, doses in the range of 10–500 mg mAb per week are effective and well tolerated. Moreover, an initial loading dose of approximately 4 mg/kg patient body weight IV, followed by weekly doses of about 2 mg/kg IV of the anti-161P2F10B mAb preparation represents an acceptable dosing regimen. As appreciated by those of skill in the art, various factors can influence the ideal dose in a particular case. Such factors include, for example, half life of a composition, the binding affinity of an Ab, the immunogenicity of a substance, the degree of 161P2F10B expression in the patient, the extent of circulating shed 161P2F10B antigen, the desired steady-state concentration level, frequency of treatment, and the influence of chemotherapeutic or other agents used in combination with the treatment method of the invention, as well as the health status of a particular patient. Non-limiting preferred human unit doses are, for example, 500 μg–1 mg, 1 mg–50 mg, 50 mg–100 mg, 100 mg–200 mg, 200 mg–300 mg, 400 mg–500 mg, 500 mg–600 mg, 600 mg–700 mg, 700 mg–800 mg, 800 mg–900 mg, 900 mg–1 g, or 1 mg–700 mg. In certain embodiments, the dose is in a range of 2–5 mg/kg body weight, e.g., with follow on weekly doses of 1–3 mg/kg; 0.5 mg, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 mg/kg body weight followed, e.g., in two, three or four weeks by weekly doses; 0.5–10 mg/kg body weight, e.g., followed in two, three or four weeks by weekly doses; 225, 250, 275, 300, 325, 350, 375, 400 mg m² of body area weekly; 1–600 mg m² of body area weekly; 225–400 mg m² of body area weekly; these does can be followed by weekly doses for 2, 3, 4, 5, 6, 7, 8, 9, 19, 11, 12 or more weeks.

In one embodiment, human unit dose forms of polynucleotides comprise a suitable dosage range or effective amount that provides any therapeutic effect. As appreciated by one of ordinary skill in the art a therapeutic effect depends on a number of factors, including the sequence of the polynucleotide, molecular weight of the polynucleotide and route of administration. Dosages are generally selected by the physician or other health care professional in accordance with a variety of parameters known in the art, such as severity of symptoms, history of the patient and the like. Generally, for a polynucleotide of about 20 bases, a dosage range may be selected from, for example, an independently selected lower limit such as about 0.1, 0.25, 0.5, 1, 2, 5,10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400 or 500 mg/kg up to an independently selected upper limit, greater than the lower limit, of about 60, 80, 100, 200, 300, 400, 500, 750, 1000, 1500, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000 or 10,000 mg/kg. For example, a dose may be about any of the following: 0.1 to 100 mg/kg, 0.1 to 50 mg/kg, 0.1 to 25 mg/kg, 0.1 to 10 mg/kg, 1 to 500 mg/kg, 100 to 400 mg/kg, 200 to 300 mg/kg, 1 to 100 mg/kg, 100 to 200 mg/kg, 300 to 400 mg/kg, 400 to 500 mg/kg, 500 to 1000 mg/kg, 500 to 5000 mg/kg, or 500 to 10,000 mg/kg. Generally, parenteral routes of administration may require higher doses of polynucleotide compared to more direct application to the nucleotide to diseased tissue, as do polynucleotides of increasing length.

In one embodiment, human unit dose forms of T-cells comprise a suitable dosage range or effective amount that provides any therapeutic effect. As appreciated by one of ordinary skill in the art, a therapeutic effect depends on a number of factors. Dosages are generally selected by the physician or other health care professional in accordance with a variety of parameters known in the art, such as severity of symptoms, history of the patient and the like. A dose may be about 10⁴ cells to about 10⁶ cells, about 10⁶ cells to about 10⁸ cells, about 10⁸ to about 10¹¹ cells, or about 10⁸ to about 5×10¹⁰ cells. A dose may also about 10⁶ cells/m² to about 10¹⁰ cells/m², or about 10⁶ cells/m² to about 10⁸ cells/m².

Proteins(s) of the invention, and/or nucleic acids encoding the protein(s), can also be administered via liposomes, which may also serve to: 1) target the proteins(s) to a particular tissue, such as lymphoid tissue; 2) to target selectively to diseases cells; or, 3) to increase the half-life of the peptide composition. Liposomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like. In these preparations, the peptide to be delivered is incorporated as part of a liposome, alone or in conjunction with a molecule which binds to a receptor prevalent among lymphoid cells, such as monoclonal antibodies which bind to the CD45 antigen, or with other therapeutic or immunogenic compositions. Thus, liposomes either filled or decorated with a desired peptide of the invention can be directed to the site of lymphoid cells, where the liposomes then deliver the peptide compositions. Liposomes for use in accordance with the invention are formed from standard vesicle-forming lipids, which generally include neutral and negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally guided by consideration of, e.g., liposome size, acid lability and stability of the liposomes in the blood stream. A variety of methods are available for preparing liposomes, as described in, e.g., Szoka, et al., Ann. Rev. Biophys. Bioeng. 9:467 (1980), and U.S. Pat. Nos. 4,235,871, 4,501,728, 4,837,028, and 5,019,369.

For targeting cells of the immune system, a ligand to be incorporated into the liposome can include, e.g., antibodies or fragments thereof specific for cell surface determinants of the desired immune system cells. A liposome suspension containing a peptide may be administered intravenously, locally, topically, etc. in a dose which varies according to, inter alia, the manner of administration, the peptide being delivered, and the stage of the disease being treated.

For solid compositions, conventional nontoxic solid carriers may be used which include, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like. For oral administration, a pharmaceutically acceptable nontoxic composition is formed by incorporating any of the normally employed excipients, such as those carriers previously listed, and generally 10–95% of active ingredient, that is, one or more peptides of the invention, and more preferably at a concentration of 25%–75%.

For aerosol administration, immunogenic peptides are preferably supplied in finely divided form along with a surfactant and propellant. Typical percentages of peptides are about 0.01%–20% by weight, preferably about 1%–10%. The surfactant must, of course, be nontoxic, and preferably soluble in the propellant. Representative of such agents are the esters or partial esters of fatty acids containing from about 6 to 22 carbon atoms, such as caproic, octanoic, lauric, palmitic, stearic, linoleic, linolenic, olesteric and oleic acids with an aliphatic polyhydric alcohol or its cyclic anhydride. Mixed esters, such as mixed or natural glycerides may be employed. The surfactant may constitute about 0.1%–20% by weight of the composition, preferably about 0.25–5%. The balance of the composition is ordinarily propellant. A carrier can also be included, as desired, as with, e.g., lecithin for intranasal delivery.

XI.) Diagnostic and Prognostic Embodiments of 161P2F10B.

As disclosed herein, 161P2F10B polynucleotides, polypeptides, reactive cytotoxic T cells (CTL), reactive helper T cells (HTL) and anti-polypeptide antibodies are used in well known diagnostic, prognostic and therapeutic assays that examine conditions associated with dysregulated cell growth such as cancer, in particular the cancers listed in Table I (see, e.g., both its specific pattern of tissue expression as well as its overexpression in certain cancers as described for example in the Example entitled “Expression analysis of 161P2F10B in normal tissues, and patient specimens”).

161P2F10B can be analogized to a prostate associated antigen PSA, the archetypal marker that has been used by medical practitioners for years to identify and monitor the presence of prostate cancer (see, e.g., Merrill et al., J. Urol. 163(2): 503–5120 (2000); Polascik et al., J. Urol. August; 162(2):293–306 (1999) and Fortier et al., J. Nat. Cancer Inst. 91(19): 1635–1640(1999)). A variety of other diagnostic markers are also used in similar contexts including p53 and K-ras (see, e.g., Tulchinsky et al., Int J Mol Med 1999 Jul 4(1):99–102 and Minimoto et al., Cancer Detect Prev 2000; 24(1):1–12). Therefore, this disclosure of 161P2F10B polynucleotides and polypeptides (as well as 161P2F10B polynucleotide probes and anti-161P2F10B antibodies used to identify the presence of these molecules) and their properties allows skilled artisans to utilize these molecules in methods that are analogous to those used, for example, in a variety of diagnostic assays directed to examining conditions associated with cancer.

Typical embodiments of diagnostic methods which utilize the 161P2F10B polynucleotides, polypeptides, reactive T cells and antibodies are analogous to those methods from well-established diagnostic assays, which employ, e.g., PSA polynucleotides, polypeptides, reactive T cells and antibodies. For example, just as PSA polynucleotides are used as probes (for example in Northern analysis, see, e.g., Sharief et al., Biochem. Mol. Biol. Int. 33(3):567–74(1994)) and primers (for example in PCR analysis, see, e.g., Okegawa et al., J. Urol. 163(4): 1189–1190 (2000)) to observe the presence and/or the level of PSA mRNAs in methods of monitoring PSA overexpression or the metastasis of prostate cancers, the 161P2F10B polynucleotides described herein can be utilized in the same way to detect 161P2F10B overexpression or the metastasis of prostate and other cancers expressing this gene. Alternatively, just as PSA polypeptides are used to generate antibodies specific for PSA which can then be used to observe the presence and/or the level of PSA proteins in methods to monitor PSA protein overexpression (see, e.g., Stephan et al., Urology 55(4):560–3 (2000)) or the metastasis of prostate cells (see, e.g., Alanen et al., Pathol. Res. Pract. 192(3):233–7 (1996)), the 161P2F10B polypeptides described herein can be utilized to generate antibodies for use in detecting 161P2F10B overexpression or the metastasis of prostate cells and cells of other cancers expressing this gene.

Specifically, because metastases involves the movement of cancer cells from an organ of origin (such as the lung or prostate gland etc) to a different area of the body (such as a lymph node), assays which examine a biological sample for the presence of cells expressing 161P2F10B polynucleotides and/or polypeptides can be used to provide evidence of metastasis. For example, when a biological sample from tissue that does not normally contain 161P2F10B-expressing cells (lymph node) is found to contain 161P2F10B-expressing cells such as the 161P2F10B expression seen in LAPC4 and LAPC9, xenografts isolated from lymph node and bone metastasis, respectively, this finding is indicative of metastasis.

Alternatively 161P2F10B polynucleotides and/or polypeptides can be used to provide evidence of cancer, for example, when cells in a biological sample that do not normally express 161P2F10B or express 161P2F10B at a different level are found to express 161P2F10B or have an increased expression of 161P2F10B (see, e.g., the 161P2F10B expression in the cancers listed in Table I and in patient samples etc. shown in the accompanying Figures). In such assays, artisans may further wish to generate supplementary evidence of metastasis by testing the biological sample for the presence of a second tissue restricted marker (in addition to 161P2F10B) such as PSA, PSCA etc. (see, e.g., Alanen et al., Pathol. Res. Pract. 192(3): 233–237 (1996)).

Just as PSA polynucleotide fragments and polynucleotide variants are employed by skilled artisans for use in methods of monitoring PSA, 161P2F10B polynucleotide fragments and polynucleotide variants are used in an analogous manner. In particular, typical PSA polynucleotides used in methods of monitoring PSA are probes or primers which consist of fragments of the PSA cDNA sequence. Illustrating this, primers used to PCR amplify a PSA polynucleotide must include less than the whole PSA sequence to function in the polymerase chain reaction. In the context of such PCR reactions, skilled artisans generally create a variety of different polynucleotide fragments that can be used as primers in order to amplify different portions of a polynucleotide of interest or to optimize amplification reactions (see, e.g., Caetano-Anolles, G. Biotechniques 25(3): 472–476, 478–480 (1998); Robertson et al., Methods Mol. Biol. 98:121–154 (1998)). An additional illustration of the use of such fragments is provided in the Example entitled “Expression analysis of 161P2F10B in normal tissues, and patient specimens,” where a 161P2F10B polynucleotide fragment is used as a probe to show the expression of 161P2F10B RNAs in cancer cells. In addition, variant polynucleotide sequences are typically used as primers and probes for the corresponding mRNAs in PCR and Northern analyses (see, e.g., Sawai et al., Fetal Diagn. Ther. 1996 Nov–Dec 11 (6):407–13 and Current Protocols In Molecular Biology, Volume 2, Unit 2, Frederick M. Ausubel et al. eds., 1995)). Polynucleotide fragments and variants are useful in this context where they are capable of binding to a target polynucleotide sequence (e.g., a 161P2F10B polynucleotide shown in FIG. 2 or variant thereof) under conditions of high stringency.

Furthermore, PSA polypeptides which contain an epitope that can be recognized by an antibody or T cell that specifically binds to that epitope are used in methods of monitoring PSA. 161P2F10B polypeptide fragments and polypeptide analogs or variants can also be used in an analogous manner. This practice of using polypeptide fragments or polypeptide variants to generate antibodies (such as anti-PSA antibodies or T cells) is typical in the art with a wide variety of systems such as fusion proteins being used by practitioners (see, e.g., Current Protocols In Molecular Biology, Volume 2, Unit 16, Frederick M. Ausubel et al. eds., 1995). In this context, each epitope(s) functions to provide the architecture with which an antibody or T cell is reactive. Typically, skilled artisans create a variety of different polypeptide fragments that can be used in order to generate immune responses specific for different portions of a polypeptide of interest (see, e.g., U.S. Pat. No. 5,840,501 and U.S. Pat. No. 5,939,533). For example it may be preferable to utilize a polypeptide comprising one of the 161P2F10B biological motifs discussed herein or a motif-bearing subsequence which is readily identified by one of skill in the art based on motifs available in the art. Polypeptide fragments, variants or analogs are typically useful in this context as long as they comprise an epitope capable of generating an antibody or T cell specific for a target polypeptide sequence (e.g. a 161P2F10B polypeptide shown in FIG. 3).

As shown herein, the 161P2F10B polynucleotides and polypeptides (as well as the 161P2F10B polynucleotide probes and anti-161P2F10B antibodies or T cells used to identify the presence of these molecules) exhibit specific properties that make them useful in diagnosing cancers such as those listed in Table I. Diagnostic assays that measure the presence of 161P2F10B gene products, in order to evaluate the presence or onset of a disease condition described herein, such as prostate cancer, are used to identify patients for preventive measures or further monitoring, as has been done so successfully with PSA. Moreover, these materials satisfy a need in the art for molecules having similar or complementary characteristics to PSA in situations where, for example, a definite diagnosis of metastasis of prostatic origin cannot be made on the basis of a test for PSA alone (see, e.g., Alanen et al., Pathol. Res. Pract. 192(3): 233–237 (1996)), and consequently, materials such as 161P2F10B polynucleotides and polypeptides (as well as the 161P2F10B polynucleotide probes and anti-161P2F10B antibodies used to identify the presence of these molecules) need to be employed to confirm a metastases of prostatic origin.

Finally, in addition to their use in diagnostic assays, the 161P2F10B polynucleotides disclosed herein have a number of other utilities such as their use in the identification of oncogenetic associated chromosomal abnormalities in the chromosomal region to which the 161P2F10B gene maps (see the Example entitled “Chromosomal Mapping of 161P2F10B” below). Moreover, in addition to their use in diagnostic assays, the 161P2F10B-related proteins and polynucleotides disclosed herein have other utilities such as their use in the forensic analysis of tissues of unknown origin (see, e.g., Takahama K Forensic Sci Int 1996 Jun. 28;80(1–2): 63–9).

Additionally, 161P2F10B-related proteins or polynucleotides of the invention can be used to treat a pathologic condition characterized by the over-expression of 161P2F10B. For example, the amino acid or nucleic acid sequence of FIG. 2 or FIG. 3, or fragments of either, can be used to generate an immune response to a 161P2F10B antigen. Antibodies or other molecules that react with 161P2F10B can be used to modulate the function of this molecule, and thereby provide a therapeutic benefit.

XII.) Inhibition of 161P2F10B Protein Function

The invention includes various methods and compositions for inhibiting the binding of 161P2F10B to its binding partner or its association with other protein(s) as well as methods for inhibiting 161P2F10B function.

XII.A.) Inhibition of 161P2F10B with Intracellular Antibodies

In one approach, a recombinant vector that encodes single chain antibodies that specifically bind to 161P2F10B are introduced into 161P2F10B expressing cells via gene transfer technologies. Accordingly, the encoded single chain anti-161P2F10B antibody is expressed intracellularly, binds to 161P2F10B protein, and thereby inhibits its function. Methods for engineering such intracellular single chain antibodies are well known. Such intracellular antibodies, also known as “intrabodies”, are specifically targeted to a particular compartment within the cell, providing control over where the inhibitory activity of-the treatment is focused. This technology has been successfully applied in the art (for review, see Richardson and Marasco, 1995, TIBTECH vol. 13). Intrabodies have been shown to virtually eliminate the expression of otherwise abundant cell surface receptors (see, e.g., Richardson et al., 1995, Proc. Natl. Acad. Sci. USA 92: 3137–3141; Beerli et al., 1994, J. Biol. Chem. 289: 23931–23936; Deshane et al., 1994, Gene Ther. 1: 332–337).

Single chain antibodies comprise the variable domains of the heavy and light chain joined by a flexible linker polypeptide, and are expressed as a single polypeptide. Optionally, single chain antibodies are expressed as a single chain variable region fragment joined to the light chain constant region. Well-known intracellular trafficking signals are engineered into recombinant polynucleotide vectors encoding such single chain antibodies in order to target precisely the intrabody to the desired intracellular compartment. For example, intrabodies targeted to the endoplasmic reticulum (ER) are engineered to incorporate a leader peptide and, optionally, a C-terminal ER retention signal, such as the KDEL amino acid motif. Intrabodies intended to exert activity in the nucleus are engineered to include a nuclear localization signal. Lipid moieties are joined to intrabodies in order to tether the intrabody to the cytosolic side of the plasma membrane. Intrabodies can also be targeted to exert function in the cytosol. For example, cytosolic intrabodies are used to sequester factors within the cytosol, thereby preventing them from being transported to their natural cellular destination.

In one embodiment, intrabodies are used to capture 161P2F10B in the nucleus, thereby preventing its activity within the nucleus. Nuclear targeting signals are engineered into such 161P2F10B intrabodies in order to achieve the desired targeting. Such 161P2F10B intrabodies are designed to bind specifically to a particular 161P2F10B domain. In another embodiment, cytosolic intrabodies that specifically bind to a 161P2F10B protein are used to prevent 161P2F10B from gaining access to the nucleus, thereby preventing it from exerting any biological activity within the nucleus (e.g., preventing 161P2F10B from forming transcription complexes with other factors).

In order to specifically direct the expression of such intrabodies to particular cells, the transcription of the intrabody is placed under the regulatory control of an appropriate tumor-specific promoter and/or enhancer. In order to target intrabody expression specifically to prostate, for example, the PSA promoter and/or promoter/enhancer can be utilized (See, for example, U.S. Pat. No. 5,919,652 issued 6 Jul. 1999).

XII.B.) Inhibition of 161P2F10B with Recombinant Proteins

In another approach, recombinant molecules bind to 161P2F10B and thereby inhibit 161P2F10B function. For example, these recombinant molecules prevent or inhibit 161P2F10B from accessing/binding to its binding partner(s) or associating with other protein(s). Such recombinant molecules can, for example, contain the reactive part(s) of a 161P2F10B specific antibody molecule. In a particular embodiment, the 161P2F10B binding domain of a 161P2F10B binding partner is engineered into a dimeric fusion protein, whereby the fusion protein comprises two 161P2F10B ligand binding domains linked to the Fc portion of a human IgG, such as human IgG1. Such IgG portion can contain, for example, the C_(H)2 and C_(H)3 domains and the hinge region, but not the CH1 domain. Such dimeric fusion proteins are administered in soluble form to patients suffering from a cancer associated with the expression of 161P2F10B, whereby the dimeric fusion protein specifically binds to 161P2F10B and blocks 161P2F10B interaction with a binding partner. Such dimeric fusion proteins are further combined into multimeric proteins using known antibody linking technologies.

XII.C.) Inhibition of 161P2F10B Transcription or Translation

The present invention also comprises various methods and compositions for inhibiting the transcription of the 161P2F10B gene. Similarly, the invention also provides methods and compositions for inhibiting the translation of 161P2F10B mRNA into protein.

In one approach, a method of inhibiting the transcription of the 161P2F10B gene comprises contacting the 161P2F10B gene with a 161P2F10B antisense polynucleotide. In another approach, a method of inhibiting 161P2F10B mRNA translation comprises contacting a 161P2F10B mRNA with an antisense polynucleotide. In another approach, a 161P2F10B specific ribozyme is used to cleave a 161P2F10B message, thereby inhibiting translation. Such antisense and ribozyme based methods can also be directed to the regulatory regions of the 161P2F10B gene, such as 161P2F10B promoter and/or enhancer elements. Similarly, proteins capable of inhibiting a 161P2F10B gene transcription factor are used to inhibit 161P2F10B mRNA transcription. The various polynucleotides and compositions useful in the aforementioned methods have been described above. The use of antisense and ribozyme molecules to inhibit transcription and translation is well known in the art.

Other factors that inhibit the transcription of 161P2F10B by interfering with 161P2F10B transcriptional activation are also useful to treat cancers expressing 161P2F10B. Similarly, factors that interfere with 161P2F10B processing are useful to treat cancers that express 161P2F10B. Cancer treatment methods utilizing such factors are also within the scope of the invention.

XII.D.) General Considerations for Therapeutic Strategies

Gene transfer and gene therapy technologies can be used to deliver therapeutic polynucleotide molecules to tumor cells synthesizing 161P2F10B (i.e., antisense, ribozyme, polynucleotides encoding intrabodies and other 161P2F10B inhibitory molecules). A number of gene therapy approaches are known in the art. Recombinant vectors encoding 161P2F10B antisense polynucleotides, ribozymes, factors capable of interfering with 161P2F10B transcription, and so forth, can be delivered to target tumor cells using such gene therapy approaches.

The above therapeutic approaches can be combined with any one of a wide variety of surgical, chemotherapy or radiation therapy regimens. The therapeutic approaches of the invention can enable the use of reduced dosages of chemotherapy (or other therapies) and/or less frequent administration, an advantage for all patients and particularly for those that do not tolerate the toxicity of the chemotherapeutic agent well.

The anti-tumor activity of a particular composition (e.g., antisense, ribozyme, intrabody), or a combination of such compositions, can be evaluated using various in vitro and in vivo assay systems. In vitro assays that evaluate therapeutic activity include cell growth assays, soft agar assays and other assays indicative of tumor promoting activity, binding assays capable of determining the extent to which a therapeutic composition will inhibit the binding of 161P2F10B to a binding partner, etc.

In vivo, the effect of a 161P2F10B therapeutic composition can be evaluated in a suitable animal model. For example, xenogenic prostate cancer models can be used, wherein human prostate cancer explants or passaged xenograft tissues are introduced into immune compromised animals, such as nude or SCID mice (Klein et al., 1997, Nature Medicine 3: 402–408). For example, PCT Patent Application WO98/16628 and U.S. Pat. No. 6,107,540 describe various xenograft models of human prostate cancer capable of recapitulating the development of primary tumors, micrometastasis, and the formation of osteoblastic metastases characteristic of late stage disease. Efficacy can be predicted using assays that measure inhibition of tumor formation, tumor regression or metastasis, and the like.

In vivo assays that evaluate the promotion of apoptosis are useful in evaluating therapeutic compositions. In one embodiment, xenografts from tumor bearing mice treated with the therapeutic composition can be examined for the presence of apoptotic foci and compared to untreated control xenograft-bearing mice. The extent to which apoptotic foci are found in the tumors of the treated mice provides an indication of the therapeutic efficacy of the composition.

The therapeutic compositions used in the practice of the foregoing methods can be formulated into pharmaceutical compositions comprising a carrier suitable for the desired delivery method. Suitable carriers include any material that when combined with the therapeutic composition retains the anti-tumor function of the therapeutic composition and is generally non-reactive with the patient's immune system. Examples include, but are not limited to, any of a number of standard pharmaceutical carriers such as sterile phosphate buffered saline solutions, bacteriostatic water, and the like (see, generally, Remington's Pharmaceutical Sciences 16th Edition, A. Osal., Ed., 1980).

Therapeutic formulations can be solubilized and administered via any route capable of delivering the therapeutic composition to the tumor site. Potentially effective routes of administration include, but are not limited to, intravenous, parenteral, intraperitoneal, intramuscular, intratumor, intradermal, intraorgan, orthotopic, and the like. A preferred formulation for intravenous injection comprises the therapeutic composition in a solution of preserved bacteriostatic water, sterile unpreserved water, and/or diluted in polyvinylchloride or polyethylene bags containing 0.9% sterile Sodium Chloride for Injection, USP. Therapeutic protein preparations can be lyophilized and stored as sterile powders, preferably under vacuum, and then reconstituted in bacteriostatic water (containing for example, benzyl alcohol preservative) or in sterile water prior to injection.

Dosages and administration protocols for the treatment of cancers using the foregoing methods will vary with the method and the target cancer, and will generally depend on a number of other factors appreciated in the art.

XIII.) Identification, Characterization and Use of Modulators of 161P2F10b

Methods to Identify and Use Modulators

In one embodiment, screening is performed to identify modulators that induce or suppress a particular expression profile, suppress or induce specific pathways, preferably generating the associated phenotype thereby. In another embodiment, having identified differentially expressed genes important in a particular state; screens are performed to identify modulators that alter expression of individual genes, either increase or decrease. In another embodiment, screening is performed to identify modulators that alter a biological function of the expression product of a differentially expressed gene. Again, having identified the importance of a gene in a particular state, screens are performed to identify agents that bind and/or modulate the biological activity of the gene product.

In addition, screens are done for genes that are induced in response to a candidate agent. After identifying a modulator (one that suppresses a cancer expression pattern leading to a normal expression palem, or a modulator of a cancer gene that leads to expression of the gene as in normal tissue) a screen is performed to identify genes that are specifically modulated in response to the agent. Comparing expression profiles between normal tissue and agent-treated cancer tissue reveals genes that are not expressed in normal tissue or cancer tissue, but are expressed in agent treated tissue, and vice versa. These agent-specific sequences are identified and used by methods described herein for cancer genes or proteins. In particular these sequences and the proteins they encode are used in marking or identifying agent-treated cells. In addition, antibodies are raised against the agent-induced proteins and used to target novel therapeutics to the treated cancer tissue sample.

Modulator-related Identification and Screening Assays:

Gene Expression-related Assays

Proteins, nucleic acids, and antibodies of the invention are used in screening assays. The cancer-associated proteins, antibodies, nucleic acids, modified proteins and cells containing these sequences are used in screening assays, such as evaluating the effect of drug candidates on a “gene expression profile,” expression profile of polypeptides or alteration of biological function. In one embodiment, the expression profiles are used, preferably in conjunction with high throughput screening techniques to allow monitoring for expression profile genes after treatment with a candidate agent (e.g., Davis, G F, et al, J Biol Screen 7:69 (2002); Zlokarnik, et al., Science 279:84–8 (1998); Heid, Genome Res 6:986–94, 1996).

The cancer proteins, antibodies, nucleic acids, modified proteins and cells containing the native or modified cancer proteins or genes are used in screening assays. That is, the present invention comprises methods for screening for compositions which modulate the cancer phenotype or a physiological function of a cancer protein of the invention. This is done on a gene itself or by evaluating the effect of drug candidates on a “gene expression profile” or biological function. In one embodiment, expression profiles are used, preferably in conjunction with high throughput screening techniques to allow monitoring after treatment with a candidate agent, see Zlokamik, supra.

A variety of assays are executed directed to the genes and proteins of the invention. Assays are run on an individual nucleic acid or protein level. That is, having identified a particular gene as up regulated in cancer, test compounds are screened for the ability to modulate gene expression or for binding to the cancer protein of the invention. “Modulation” in this context includes an increase or a decrease in gene expression. The preferred amount of modulation will depend on the original change of the gene expression in normal versus tissue undergoing cancer, with changes of at least 10%, preferably 50%, more preferably 100–300%, and in some embodiments 300–1000% or greater. Thus, if a gene exhibits a 4-fold increase in cancer tissue compared to normal tissue, a decrease of about four-fold is often desired; similarly, a 10-fold decrease in cancer tissue compared to normal tissue a target value of a 10-fold increase in expression by the test compound is often desired. Modulators that exacerbate the type of gene expression seen in cancer are also useful, e.g., as an upregulated target in further analyses.

The amount of gene expression is monitored using nucleic acid probes and the quantification of gene expression levels, or, alternatively, a gene product itself is monitored, e.g., through the use of antibodies to the cancer protein and standard immunoassays. Proteomics and separation techniques also allow for quantification of expression.

Expression Monitoring to Identify Compounds that Modify Gene Expression

In one embodiment, gene expression monitoring, i.e., an expression profile, is monitored simultaneously for a number of entities. Such profiles will typically involve one or more of the genes of FIG. 2. In this embodiment, e.g., cancer nucleic acid probes are attached to biochips to detect and quantify cancer sequences in a particular cell. Alternatively, PCR can be used. Thus, a series, e.g., wells of a microtiter plate, can be used with dispensed primers in desired wells. A PCR reaction can then be performed and analyzed for each well.

Expression monitoring is performed to identify compounds that modify the expression of one or more cancer-associated sequences, e.g., a polynucleotide sequence set out in FIG. 2. Generally, a test modulator is added to the cells prior to analysis. Moreover, screens are also provided to identify agents that modulate cancer, modulate cancer proteins of the invention, bind to a cancer protein of the invention, or interfere with the binding of a cancer protein of the invention and an antibody or other binding partner.

In one embodiment, high throughput screening methods involve providing a library containing a large number of potential therapeutic compounds (candidate compounds). Such “combinatorial chemical libraries” are then screened in one or more assays to identify those library members (particular chemical species or subclasses) that display a desired characteristic activity. The compounds thus identified can serve as conventional “lead compounds,” as compounds for screening, or as therapeutics.

In certain embodiments, combinatorial libraries of potential modulators are screened for an ability to bind to a cancer polypeptide or to modulate activity. Conventionally, new chemical entities with useful properties are generated by identifying a chemical compound (called a “lead compound”) with some desirable property or activity, e.g., inhibiting activity, creating variants of the lead compound, and evaluating the property and activity of those variant compounds. Often, high throughput screening (HTS) methods are employed for such an analysis.

As noted above, gene expression monitoring is conveniently used to test candidate modulators (e.g., protein, nucleic acid or small molecule). After the candidate agent has been added and the cells allowed to incubate for a period, the sample containing a target sequence to be analyzed is, e.g., added to a biochip.

If required, the target sequence is prepared using known techniques. For example, a sample is treated to lyse the cells, using known lysis buffers, electroporation, etc., with purification and/or amplification such as PCR performed as appropriate. For example, an in vitro transcription with labels covalently attached to the nucleotides is performed. Generally, the nucleic acids are labeled with biotin-FITC or PE, or with cy3 or cy5.

The target sequence can be labeled with, e.g., a fluorescent, a chemiluminescent, a chemical, or a radioactive signal, to provide a means of detecting the target sequence's specific binding to a probe. The label also can be an enzyme, such as alkaline phosphatase or horseradish peroxidase, which when provided with an appropriate substrate produces a product that is detected. Alternatively, the label is a labeled compound or small molecule, such as an enzyme inhibitor, that binds but is not catalyzed or altered by the enzyme. The label also can be a moiety or compound, such as, an epitope tag or biotin which specifically binds to streptavidin. For the example of biotin, the streptavidin is labeled as described above, thereby, providing a detectable signal for the bound target sequence. Unbound labeled streptavidin is typically removed prior to analysis.

As will be appreciated by those in the art, these assays can be direct hybridization assays or can comprise “sandwich assays”, which include the use of multiple probes, as is generally outlined in U.S. Pat. Nos. 5, 681,702; 5,597,909; 5,545,730; 5,594,117; 5,591,584; 5,571,670; 5,580,731; 5,571,670; 5,591,584; 5,624,802; 5,635,352; 5,594,118; 5,359,100; 5,124,246; and 5,681,697. In this embodiment, in general, the target nucleic acid is prepared as outlined above, and then added to the biochip comprising a plurality of nucleic acid probes, under conditions that allow the formation of a hybridization complex.

A variety of hybridization conditions are used in the present invention, including high, moderate and low stringency conditions as outlined above. The assays are generally run under stringency conditions which allow formation of the label probe hybridization complex only in the presence of target. Stringency can be controlled by altering a step parameter that is a thermodynamic variable, including, but not limited to, temperature, formamide concentration, salt concentration, chaotropic salt concentration pH, organic solvent concentration, etc. These parameters may also be used to control non-specific binding, as is generally outlined in U.S. Pat. No. 5,681,697. Thus, it can be desirable to perform certain steps at higher stringency conditions to reduce non-specific binding.

The reactions outlined herein can be accomplished in a variety of ways. Components of the reaction can be added simultaneously, or sequentially, in different orders, with preferred embodiments outlined below. In addition, the reaction may include a variety of other reagents. These include salts, buffers, neutral proteins, e.g. albumin, detergents, etc. which can be used to facilitate optimal hybridization and detection, and/or reduce nonspecific or background interactions. Reagents that otherwise improve the efficiency of the assay, such as protease inhibitors, nuclease inhibitors, anti-microbial agents, etc., may also be used as appropriate, depending on the sample preparation methods and purity of the target. The assay data are analyzed to determine the expression levels of individual genes, and changes in expression levels as between states, forming a gene expression profile.

Biological Activity-related Assays

The invention provides methods identify or screen for a compound that modulates the activity of a cancer-related gene or protein of the invention. The methods comprise adding a test compound, as defined above, to a cell comprising a cancer protein of the invention. The cells contain a recombinant nucleic acid that encodes a cancer protein of the invention. In another embodiment, a library of candidate agents is tested on a plurality of cells.

In one aspect, the assays are evaluated in the presence or absence or previous or subsequent exposure of physiological signals, e.g. hormones, antibodies, peptides, antigens, cytokines, growth factors, action potentials, pharmacological agents including chemotherapeutics, radiation, carcinogenics, or other cells (i.e., cell-cell contacts). In another example, the determinations are made at different stages of the cell cycle process. In this way, compounds that modulate genes or proteins of the invention are identified. Compounds with pharmacological activity are able to enhance or interfere with the activity of the cancer protein of the invention. Once identified, similar structures are evaluated to identify critical structural features of the compound.

In one embodiment, a method of modulating (e.g., inhibiting) cancer cell division is provided; the method comprises administration of a cancer modulator. In another embodiment, a method of modulating (e.g., inhibiting) cancer is provided; the method comprises administration of a cancer modulator. In a further embodiment, methods of treating cells or individuals with cancer are provided; the method comprises administration of a cancer modulator.

In one embodiment, a method for modulating the status of a cell that expresses a gene of the invention is provided. As used herein status comprises such art-accepted parameters such as growth, proliferation, survival, function, apoptosis, senescence, location, enzymatic activity, signal transduction, etc. of a cell. In one embodiment, a cancer inhibitor is an antibody as discussed above. In another embodiment, the cancer inhibitor is an antisense molecule. A variety of cell growth, proliferation, and metastasis assays are known to those of skill in the art, as described herein.

High Throughput Screening to Identify Modulators

The assays to identify suitable modulators are amenable to high throughput screening. Preferred assays thus detect enhancement or inhibition of cancer gene transcription, inhibition or enhancement of polypeptide expression, and inhibition or enhancement of polypeptide activity.

In one embodiment, modulators evaluated in high throughput screening methods are proteins, often naturally occurring proteins or fragments of naturally occurring proteins. Thus, e.g., cellular extracts containing proteins, or random or directed digests of proteinaceous cellular extracts, are used. In this way, libraries of proteins are made for screening in the methods of the invention. Particularly preferred in this embodiment are libraries of bacterial, fungal, viral, and mammalian proteins, with the latter being preferred, and human proteins being especially preferred. Particularly useful test compound will be directed to the class of proteins to which the target belongs, e.g., substrates for enzymes, or ligands and receptors.

Use of Soft Agar Growth and Colony Formation to Identify and Characterize Modulators

Normal cells require a solid substrate to attach and grow. When cells are transformed, they lose this phenotype and grow detached from the substrate. For example, transformed cells can grow in stirred suspension culture or suspended in semi-solid media, such as semi-solid or soft agar. The transformed cells, when transfected with tumor suppressor genes, can regenerate normal phenotype and once again require a solid substrate to attach to and grow. Soft agar growth or colony formation in assays are used to identify modulators of cancer sequences, which when expressed in host cells, inhibit abnormal cellular proliferation and transformation. A modulator reduces or eliminates the host cells' ability to grow suspended in solid or semisolid media, such as agar.

Techniques for soft agar growth or colony formation in suspension assays are described in Freshney, Culture of Animal Cells a Manual of Basic Technique (3rd ed., 1994). See also, the methods section of Garkavtsev et al. (1996), supra.

Evaluation of Contact Inhibition and Growth Density Limitation to Identify and Characterize Modulators

Normal cells typically grow in ma flat and organized pattern in cell culture until they touch other cells. When the cells touch one another, they are contact inhibited and stop growing. Transformed cells, however, are not contact inhibited and continue to grow to high densities in disorganized foci. Thus, transformed cells grow to a higher saturation density than corresponding normal cells. This is detected morphologically by the formation of a disoriented monolayer of cells or cells in foci. Alternatively, labeling index with (3H)-thymidine at saturation density is used to measure density limitation of growth, similarly an MTT or Alamar blue assay will reveal proliferation capacity of cells and the the ability of modulators to affect same. See Freshney (1994), supra. Transformed cells, when transfected with tumor suppressor genes, can regenerate a normal phenotype and become contact inhibited and would grow to a lower density.

In this assay, labeling index with ³H)-thymidine at saturation density is a preferred method of measuring density limitation of growth. Transformed host cells are transfected with a cancer-associated sequence and are grown for 24 hours at saturation density in non-limiting medium conditions. The percentage of cells labeling with (³H)-thymidine is determined by incorporated cpm.

Contact independent growth is used to identify modulators of cancer sequences, which had led to abnormal cellular proliferation and transformation. A modulator reduces or eliminates contact independent growth, and returns the cells to a normal phenotype.

Evaluation of Growth Factor or Serum Dependence to Identify and Characterize Modulators

Transformed cells have lower serum dependence than their normal counterparts (see, e.g., Temin, J. Natl. Cancer Inst. 37:167–175 (1966); Eagle et al., J. Exp. Med 131:836–879 (1970)); Freshney, supra. This is in part due to release of various growth factors by the transformed cells. The degree of growth factor or serum dependence of transformed host cells can be compared with that of control. For example, growth factor or serum dependence of a cell is monitored in methods to identify and characterize compounds that modulate cancer-associated sequences of the invention.

Use of Tumor-Specific Marker Levels to Identify and Characterize Modulators

Tumor cells release an increased amount of certain factors (hereinafter “tumor specific markers”) than their normal counterparts. For example, plasminogen activator (PA) is released from human glioma at a higher level than from normal brain cells (see, e.g., Gullino, Angiogenesis, Tumor Vascularization, and Potential Interference with Tumor Growth, in Biological Responses in Cancer, pp. 178–184 (Mihich (ed.) 1985)). Similarly, Tumor Angiogenesis Factor (TAF) is released at a higher level in tumor cells than their normal counterparts. See, e.g., Folkman, Angiogenesis and Cancer, Sem Cancer Biol. (1992)), while bFGF is released from endothelial tumors (Ensoli, B et al).

Various techniques which measure the release of these factors are described in Freshney (1994), supra. Also, see, Unkless et al., J. Biol. Chem. 249:4295–4305 (1974); Strickland & Beers, J. Biol. Chem. 251:5694–5702 (1976); Whur et al., Br. J. Cancer 42:305 312 (1980); Gullino, Angiogenesis, Tumor Vascularization, and Potential Interference with Tumor Growth, in Biological Responses in Cancer, pp. 178–184 (Mihich (ed.) 1985); Freshney, Anticancer Res. 5:111–130 (1985). For example, tumor specific marker levels are monitored in methods to identify and characterize compounds that modulate cancer-associated sequences of the invention.

Invasiveness into Matrigel to Identify and Characterize Modulators

The degree of invasiveness into Matrigel or an extracellular matrix constituent can be used as an assay to identify and characterize compounds that modulate cancer associated sequences. Tumor cells exhibit a positive correlation between malignancy and invasiveness of cells into Matrigel or some other extracellular matrix constituent. In this assay, tumorigenic cells are typically used as host cells. Expression of a tumor suppressor gene in these host cells would decrease invasiveness of the host cells. Techniques described in Cancer Res. 1999; 59:6010; Freshney (1994), supra, can be used. Briefly, the level of invasion of host cells is measured by using filters coated with Matrigel or some other extracellular matrix constituent. Penetration into the gel, or through to the distal side of the filter, is rated as invasiveness, and rated histologically by number of cells and distance moved, or by prelabeling the cells with ¹²⁵1 and counting the radioactivity on the distal side of the filter or bottom of the dish. See, e.g., Freshney (1984), supra.

Evaluation of Tumor Growth In Vivo to Identify and Characterize Modulators

Effects of cancer-associated sequences on cell growth are tested in transgenic or immune-suppressed organisms. Transgenic organisms are prepared in a variety of art-accepted ways. For example, knock-out transgenic organisms, e.g., mammals such as mice, are made, in which a cancer gene is disrupted or in which a cancer gene is inserted. Knock-out transgenic mice are made by insertion of a marker gene or other heterologous gene into the endogenous cancer gene site in the mouse genome via homologous recombination. Such mice can also be made by substituting the endogenous cancer gene with a mutated version of the cancer gene, or by mutating the endogenous cancer gene, e.g., by exposure to carcinogens.

To prepare transgenic chimeric animals, e.g., mice, a DNA construct is introduced into the nuclei of embryonic stem cells. Cells containing the newly engineered genetic lesion are injected into a host mouse embryo, which is re-implanted into a recipient female. Some of these embryos develop into chimeric mice that possess germ cells some of which are derived from the mutant cell line. Therefore, by breeding the chimeric mice it is possible to obtain a new line of mice containing the introduced genetic lesion (see, e.g., Capecchi et al., Science 244:1288 (1989)). Chimeric mice can be derived according to U.S. Pat. No. 6,365,797, issued 2 Apr. 2002; U.S. Pat. No. 6,107,540 issued 22 Aug. 2000; Hogan et al., Manipulating the Mouse Embryo: A laboratory Manual, Cold Spring Harbor Laboratory (1988) and Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, Robertson, ed., IRL Press, Washington, D.C., (1987).

Alternatively, various immune-suppressed or immune-deficient host animals can be used. For example, a genetically athymic “nude” mouse (see, e.g., Giovanella et al., J. Natl. Cancer Inst. 52:921 (1974)), a SCID mouse, a thymectornized mouse, or an irradiated mouse (see, e.g., Bradley et al., Br. J. Cancer 38:263 (1978); Selby et al., Br. J. Cancer 41:52 (1980)) can be used as a host. Transplantable tumor cells (typically about 10⁶ cells) injected into isogenic hosts produce invasive tumors in a high proportion of cases, while normal cells of similar origin will not. In hosts which developed invasive tumors, cells expressing cancer-associated sequences are injected subcutaneously or orthotopically. Mice are then separated into groups, including control groups and treated experimental groups) e.g. treated with a modulator). After a suitable length of time, preferably 4–8 weeks, tumor growth is measured (e.g., by volume or by its two largest dimensions, or weight) and compared to the control. Tumors that have statistically significant reduction (using, e.g., Students T test) are said to have inhibited growth.

In Vitro Assays to Identify and Characterize Modulators

Assays to identify compounds with modulating activity can be performed in vitro. For example, a cancer polypeptide is first contacted with a potential modulator and incubated for a suitable amount of time, e.g., from 0.5 to 48 hours. In one embodiment, the cancer polypeptide levels are determined in vitro by measuring the level of protein or mRNA. The level of protein is measured using immunoassays such as Western blotting, ELISA and the like with an antibody that selectively binds to the cancer polypeptide or a fragment thereof. For measurement of mRNA, amplification, e.g., using PCR, LCR, or hybridization assays, e.g., Northern hybridization, RNAse protection, dot blotting, are preferred. The level of protein or mRNA is detected using directly or indirectly labeled detection agents, e.g., fluorescently or radioactively labeled nucleic acids, radioactively or enzymatically labeled antibodies, and the like, as described herein.

Alternatively, a reporter gene system can be devised using a cancer protein promoter operably linked to a reporter gene such as luciferase, green fluorescent protein, CAT, or P-gal. The reporter construct is typically transfected into a cell. After treatment with a potential modulator, the amount of reporter gene transcription, translation, or activity is measured according to standard techniques known to those of skill in the art (Davis GF, supra; Gonzalez, J. & Negulescu, P. Curr. Opin. Biotechnol. 1998: 9:624).

As outlined above, in vitro screens are done on individual genes and gene products. That is, having identified a particular differentially expressed gene as important in a particular state, screening of modulators of the expression of the gene or the gene product itself is performed.

In one embodiment, screening for modulators of expression of specific gene(s) is performed. Typically, the expression of only one or a few genes is evaluated. In another embodiment, screens are designed to first find compounds that bind to differentially expressed proteins. These compounds are then evaluated for the ability to modulate differentially expressed activity. Moreover, once initial candidate compounds are identified, variants can be further screened to better evaluate structure activity relationships.

Binding Assays to Identify and Characterize Modulators

In binding assays in accordance with the invention, a purified or isolated gene product of the invention is generally used. For example, antibodies are generated to a protein of the invention, and immunoassays are run to determine the amount and/or location of protein. Alternatively, cells comprising the cancer proteins are used in the assays.

Thus, the methods comprise combining a cancer protein of the invention and a candidate compound such as a ligand, and determining the binding of the compound to the cancer protein of the invention. Preferred embodiments utilize the human cancer protein; animal models of human disease of can also be developed and used. Also, other analogous mammalian proteins also can be used as appreciated by those of skill in the art. Moreover, in some embodiments variant or derivative cancer proteins are used.

Generally, the cancer protein of the invention, or the ligand, is non-diffusibly bound to an insoluble support. The support can, e.g., be one having isolated sample receiving areas (a microtiter plate, an array, etc.). The insoluble supports can be made of any composition to which the compositions can be bound, is readily separated from soluble material, and is otherwise compatible with the overall method of screening. The surface of such supports can be solid or porous and of any convenient shape.

Examples of suitable insoluble supports include microtiter plates, arrays, membranes and beads. These are typically made of glass, plastic (e.g., polystyrene), polysaccharide, nylon, nitrocellulose, or Teflon M, etc. Microtiter plates and arrays are especially convenient because a large number of assays can be carried out simultaneously, using small amounts of reagents and samples. The particular manner of binding of the composition to the support is not crucial so long as it is compatible with the reagents and overall methods of the invention, maintains the activity of the composition and is nondiffusable. Preferred methods of binding include the use of antibodies which do not sterically block either the ligand binding site or activation sequence when attaching the protein to the support, direct binding to “sticky” or ionic supports, chemical crosslinking, the synthesis of the protein or agent on the surface, etc. Following binding of the protein or ligand/binding agent to the support, excess unbound material is removed by washing. The sample receiving areas may then be blocked through incubation with bovine serum albumin (BSA), casein or other innocuous protein or other moiety.

Once a cancer protein of the invention is bound to the support, and a test compound is added to the assay. Alternatively, the candidate binding agent is bound to the support and the cancer protein of the invention is then added. Binding agents include specific antibodies, non-natural binding agents identified in screens of chemical libraries, peptide analogs, etc.

Of particular interest are assays to identify agents that have a low toxicity for human cells. A wide variety of assays can be used for this purpose, including proliferation assays, cAMP assays, labeled in vitro protein-protein binding assays, electrophoretic mobility shift assays, immunoassays for protein binding, functional assays (phosphorylation assays, etc.) and the like.

A determination of binding of the test compound (ligand, binding agent, modulator, etc.) to a cancer protein of the invention can be done in a number of ways. The test compound can be labeled, and binding determined directly, e.g., by attaching all or a portion of the cancer protein of the invention to a solid support, adding a labeled candidate compound (e.g., a fluorescent label), washing off excess reagent, and determining whether the label is present on the solid support. Various blocking and washing steps can be utilized as appropriate.

In certain embodiments, only one of the components is labeled, e.g., a protein of the invention or ligands labeled. Alternatively, more than one component is labeled with different labels, e.g., I¹²⁵, for the proteins and a fluorophor for the compound. Proximity reagents, e.g., quenching or energy transfer reagents are also useful.

Competitive Binding to Identify and Characterize Modulators

In one embodiment, the binding of the “test compound” is determined by competitive binding assay with a competitor. The competitor is a binding moiety that binds to the target molecule (e.g., a cancer protein of the invention). Competitors include compounds such as antibodies, peptides, binding partners, ligands, etc. Under certain circumstances, the competitive binding between the test compound and the competitor displaces the test compound. In one embodiment, the test compound is labeled. Either the test compound, the competitor, or both, is added to the protein for a time sufficient to allow binding. Incubations are performed at a temperature that facilitates optimal activity, typically between four and 40° C. Incubation periods are typically optimized, e.g., to facilitate rapid high throughput screening; typically between zero and one hour will be sufficient. Excess reagent is generally removed or washed away. The second component is then added, and the presence or absence of the labeled component is followed, to indicate binding.

In one embodiment, the competitor is added first, followed by the test compound. Displacement of the competitor is an indication that the test compound is binding to the cancer protein and thus is capable of binding to, and potentially modulating, the activity of the cancer protein. In this embodiment, either component can be labeled. Thus, e.g., if the competitor is labeled, the presence of label in the post-test compound wash solution indicates displacement by the test compound. Alternatively, if the test compound is labeled, the presence of the label on the support indicates displacement.

In an alternative embodiment, the test compound is added first, with incubation and washing, followed by the competitor. The absence of binding by the competitor indicates that the test compound binds to the cancer protein with higher affinity than the competitor. Thus, if the test compound is labeled, the presence of the label on the support, coupled with a lack of competitor binding, indicates that the test compound binds to and thus potentially modulates the cancer protein of the invention.

Accordingly, the competitive binding methods comprise differential screening to identity agents that are capable of modulating the activity of the cancer proteins of the invention. In this embodiment, the methods comprise combining a cancer protein and a competitor in a first sample. A second sample comprises a test compound, the cancer protein, and a competitor. The binding of the competitor is determined for both samples, and a change, or difference in binding between the two samples indicates the presence of an agent capable of binding to the cancer protein and potentially modulating its activity. That is, if the binding of the competitor is different in the second sample relative to the first sample, the agent is capable of binding to the cancer protein.

Alternatively, differential screening is used to identify drug candidates that bind to the native cancer protein, but cannot bind to modified cancer proteins. For example the structure of the cancer protein is modeled and used in rational drug design to synthesize agents that interact with that site, agents which generally do not bind to site-modified proteins. Moreover, such drug candidates that affect the activity of a native cancer protein are also identified by screening drugs for the ability to either enhance or reduce the activity of such proteins.

Positive controls and negative controls can be used in the assays. Preferably control and test samples are performed in at least triplicate to obtain statistically significant results. Incubation of all samples occurs for a time sufficient to allow for the binding of the agent to the protein. Following incubation, samples are washed free of non-specifically bound material and the amount of bound, generally labeled agent determined. For example, where a radiolabel is employed, the samples can be counted in a scintillation counter to determine the amount of bound compound.

A variety of other reagents can be included in the screening assays. These include reagents like salts, neutral proteins, e.g. albumin, detergents, etc. which are used to facilitate optimal protein-protein binding and/or reduce non-specific or background interactions. Also reagents that otherwise improve the efficiency of the assay, such as protease inhibitors, nuclease inhibitors, anti-microbial agents, etc., can be used. The mixture of components is added in an order that provides for the requisite binding.

Use of Polynucleotides to Down-regulate or Inhibit a Protein of the Invention.

Polynucleotide modulators of cancer can be introduced into a cell containing the target nucleotide sequence by formation of a conjugate with a ligand-binding molecule, as described in WO 91/04753. Suitable ligand-binding molecules include, but are not limited to, cell surface receptors, growth factors, other cytokines, or other ligands that bind to cell surface receptors. Preferably, conjugation of the ligand binding molecule does not substantially interfere with the ability of the ligand binding molecule to bind to its corresponding molecule or receptor, or block entry of the sense or antisense oligonucleotide or its conjugated version into the cell. Alternatively, a polynucleotide modulator of cancer can be introduced into a cell containing the target nucleic acid sequence, e.g., by formation of a polynucleotide-lipid complex, as described in WO 90/10448. It is understood that the use of antisense molecules or knock out and knock in models may also be used in screening assays as discussed above, in addition to methods of treatment.

Inhibitory and Antisense Nucleotides

In certain embodiments, the activity of a cancer-associated protein is down-regulated, or entirely inhibited, by the use of antisense polynucleotide or inhibitory small nuclear RNA (snRNA), i.e., a nucleic acid complementary to, and which can preferably hybridize specifically to, a coding mRNA nucleic acid sequence, e.g., a cancer protein of the invention, mRNA, or a subsequence thereof. Binding of the antisense polynucleotide to the mRNA reduces the translation and/or stability of the mRNA.

In the context of this invention, antisense polynucleotides can comprise naturally occurring nucleotides, or synthetic species formed from naturally occurring subunits or their close homologs. Antisense polynucleotides may also have altered sugar moieties or inter-sugar linkages. Exemplary among these are the phosphorothioate and other sulfur containing species which are known for use in the art. Analogs are comprised by this invention so long as they function effectively to hybridize with nucleotides of the invention. See, e.g., Isis Pharmaceuticals, Carlsbad, Calif.; Sequitor, Inc., Natick, Mass.

Such antisense polynucleotides can readily be synthesized using recombinant means, or can be synthesized in vitro. Equipment for such synthesis is sold by several vendors, including Applied Biosystems. The preparation of other oligonucleotides such as phosphorothioates and alkylated derivatives is also well known to those of skill in the art.

Antisense molecules as used herein include antisense or sense oligonucleotides. Sense oligonucleotides can, e.g., be employed to block transcription by binding to the anti-sense strand. The antisense and sense oligonucleotide comprise a single stranded nucleic acid sequence (either RNA or DNA) capable of binding to target mRNA (sense) or DNA (antisense) sequences for cancer molecules. Antisense or sense oligonucleotides, according to the present invention, comprise a fragment generally at least about 12 nucleotides, preferably from about 12 to 30 nucleotides. The ability to derive an antisense or a sense oligonucleotide, based upon a cDNA sequence encoding a given protein is described in, e.g., Stein & Cohen (Cancer Res. 48:2659 (1988 and van der Krol et al. (BioTechniques 6:958 (1988)).

Ribozymes

In addition to antisense polynucleotides, ribozymes can be used to target and inhibit transcription of cancer-associated nucleotide sequences. A ribozyme is an RNA molecule that catalytically cleaves other RNA molecules. Different kinds of ribozymes have been described, including group I ribozymes, hammerhead ribozymes, hairpin ribozymes, RNase P, and axhead ribozymes (see, e.g.; Castanotto et al., Adv. in Pharmacology 25: 289–317 (1994) for a general review of the properties of different ribozymes).

The general features of hairpin ribozymes are described, e.g., in Hampel et al., Nucl. Acids Res. 18:299–304 (1990); European Patent Publication No. 0360257; U.S. Pat. No. 5,254,678. Methods of preparing are well known to those of skill in the art (see, e.g., WO 94/26877; Ojwang et al., Proc. Natl. Acad. Sci. USA 90:6340–6344 (1993); Yamada et al., Human Gene Therapy 1:39–45 (1994); Leavitt et al., Proc. Natl. Acad. Sci. USA 92:699–703 (1995); Leavitt et al., Human Gene Therapy 5: 1151–120 (1994); and Yamada et al., Virology 205: 121–126 (1994)).

Use of Modulators in Phenotypic Screening

In one embodiment, a test compound is administered to a population of cancer cells, which have an associated cancer expression profile. By “administration” or “contacting” herein is meant that the modulator is added to the cells in such a manner as to allow the modulator to act upon the cell, whether by uptake and intracellular action, or by action at the cell surface. In some embodiments, a nucleic acid encoding a proteinaceous agent (i.e., a peptide) is put into a viral construct such as an adenoviral or retroviral construct, and added to the cell, such that expression of the peptide agent is accomplished, e.g., PCT US97/01019. Regulatable gene therapy systems can also be used. Once the modulator has been administered to the cells, the cells are washed if desired and are allowed to incubate under preferably physiological conditions for some period. The cells are then harvested and a new gene expression profile is generated. Thus, e.g., cancer tissue is screened for agents that modulate, e.g., induce or suppress, the cancer phenotype. A change in at least one gene, preferably many, of the expression profile indicates that the agent has an effect on cancer activity. Similarly, altering a biological function or a signaling pathway is indicative of modulator activity. By defining such a signature for the cancer phenotype, screens for new drugs that alter the phenotype are devised. With this approach, the drug target need not be known and need not be represented in the original gene/protein expression screening platform, nor does the level of transcript for the target protein need to change. The modulator inhibiting function will serve as a surrogate marker

As outlined above, screens are done to assess genes or gene products. That is, having identified a particular differentially expressed gene as important in a particular state, screening of modulators of either the expression of the gene or the gene product itself is performed.

Use of Modulators to Affect Peptides of the Invention

Measurements of cancer polypeptide activity, or of the cancer phenotype are performed using a variety of assays. For example, the effects of modulators upon the function of a cancer polypeptide(s) are measured by examining parameters described above. A physiological change that affects activity is used to assess the influence of a test compound on the polypeptides of this invention. When the functional outcomes are determined using intact cells or animals, a variety of effects can be assesses such as, in the case of a cancer associated with solid tumors, tumor growth, tumor metastasis, neovascularization, hormone release, transcriptional changes to both known and uncharacterized genetic markers (e.g., by Northern blots), changes in cell metabolism such as cell growth or pH changes, and changes in intracellular second messengers such as cGNIP.

Methods of Identifying Characterizing Cancer-associated Sequences

Expression of various gene sequences is correlated with cancer. Accordingly, disorders based on mutant or variant cancer genes are determined. In one embodiment, the invention provides methods for identifying cells containing variant cancer genes, e.g., determining the presence of, all or part, the sequence of at least one endogenous cancer gene in a cell. This is accomplished using any number of sequencing techniques. The invention comprises methods of identifying the cancer genotype of an individual, e.g., determining all or part of the sequence of at least one gene of the invention in the individual. This is generally done in at least one tissue of the individual, e.g., a tissue set forth in Table I, and may include the evaluation of a number of tissues or different samples of the same tissue. The method may include comparing the sequence of the sequenced gene to a known cancer gene, i.e., a wild-type gene to determine the presence of family members, homologies, mutations or variants. The sequence of all or part of the gene can then be compared to the sequence of a known cancer gene to determine if any differences exist. This is done using any number of known homology programs, such as BLAST, Bestfit, etc. The presence of a difference in the sequence between the cancer gene of the patient and the known cancer gene correlates with a disease state or a propensity for a disease state, as outlined herein.

In a preferred embodiment, the cancer genes are used as probes to determine the number of copies of the cancer gene in the genome. The cancer genes are used as probes to determine the chromosomal localization of the cancer genes. Information such as chromosomal localization finds use in providing a diagnosis or prognosis in particular when chromosomal abnormalities such as translocations, and the like are identified in the cancer gene locus.

XIV.) Kits/Articles of Manufacture

For use in the diagnostic and therapeutic applications described herein, kits are also within the scope of the invention. Such kits can comprise a carrier, package or container that is compartmentalized to receive one or more containers such as vials, tubes, and the like, each of the container(s) comprising one of the separate elements to be used in the method. For example, the container(s) can comprise a probe that is or can be detectably labeled. Such probe can be an antibody or polynucleotide specific for a FIG. 2-related protein or a FIG. 2 gene or message, respectively. Where the method utilizes nucleic acid hybridization to detect the target nucleic acid, the kit can also have containers containing nucleotide(s) for amplification of the target nucleic acid sequence and/or a container comprising a reporter-means, such as a biotin-binding protein, such as avidin or streptavidin, bound to a reporter molecule, such as an enzymatic, florescent, or radioisotope label. The kit can include all or part of the amino acid sequences in FIG. 2 or FIG. 3 or analogs thereof, or a nucleic acid molecules that encodes such amino acid sequences.

The kit of the invention will typically comprise the container described above and one or more other containers comprising materials desirable from a commercial and user standpoint, including buffers, diluents, filters, needles, syringes; carrier, package, container, vial and/or tube labels listing contents and/or instructions for use, and package inserts with instructions for use.

A label can be present on the container to indicate that the composition is used for a specific therapy or non-therapeutic application, such as a diagnostic or laboratory application, and can also indicate directions for either in vivo or in vitro use, such as those described herein. Directions and or other information can also be included on an insert(s) or label(s) which is included with or on the kit.

The terms “kit” and “article of manufacture” can be used as synonyms.

In another embodiment of the invention, an article(s) of manufacture containing compositions, such as amino acid sequence(s), small molecule(s), nucleic acid sequence(s), and/or antibody(s), e.g., materials useful for the diagnosis, prognosis, prophylaxis and/or treatment of neoplasias of tissues such as those set forth in Table I is provided. The article of manufacture typically comprises at least one container and at least one label. Suitable containers include, for example, bottles, vials, syringes, and test tubes. The containers can be formed from a variety of materials such as glass or plastic. The container can hold amino acid sequence(s), small molecule(s), nucleic acid sequence(s), and/or antibody(s), in one embodiment the container holds a polynucleotide for use in examining the mRNA expression profile of a cell, together with reagents used for this purpose.

The container can alternatively hold a composition which is effective for treating, diagnosis, prognosing or prophylaxing a condition and can have a sterile access port (for example the container can be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle). The active agents in the composition can be an antibody capable of specifically binding 161P2F10B and modulating the function of 161P2F10B.

The label can be on or associated with the container. A label a can be on a container when letters, numbers or other characters forming the label are molded or etched into the container itself; a label can be associated with a container when it is present within a receptacle or carrier that also holds the container, e.g., as a package insert. The label can indicate that the composition is used for diagnosing, treating, prophylaxing or prognosing a condition, such as a neoplasia of a tissue set forth in Table I. The article of manufacture can further comprise a second container comprising a pharmaceutically-acceptable buffer, such as phosphate-buffered saline, Ringers solution and/ordextrose solution. It can further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, stirrers, needles, syringes, and/or package inserts with indications and/or instructions for use

EXAMPLES

Various aspects of the invention are further described and illustrated by way of the several examples that follow, none of which are intended to limit the scope of the invention.

Example 1 SSH-Generated Isolation of cDNA Fragment of the STEAP Gene

To isolate genes that are over-expressed in kidney cancer we used the Suppression Subtractive Hybridization (SSH) procedure using cDNA derived from kidney cancer patient tissues.

The 161P2F10B SSH cDNA sequence was derived from a subtraction consisting of a kidney cancer minus normal kidney and a mixture of 9 normal tissues: stomach, skeletal muscle, lung, brain, liver, kidney, pancreas, small intestine and heart. By RT-PCR, the 161P2F10B cDNA was identified as highly expressed in kidney cancer pool, with lower expression detected in prostate cancer xenograft pool, prostate cancer pool, colon cancer pool, lung cancer pool, ovary cancer pool, breast cancer pool, metastasis cancer pool, pancreas cancer pool, 2 different prostate cancer metastasis to lymph node, VP1 and VP2. (FIG. 14).

The 161P2F10B SSH cDNA sequence of 182 bp matches the cDNA for phosphodiesterase l/nucleotide pyrophosphatase 3 (PDNP3). The full-length 161P2F10B cDNA and ORF are described in FIG. 2 with the protein sequence listed in FIG. 3.

Materials and Methods

RNA Isolation:

Tumor tissues were homogenized in Trizol reagent (Life Technologies, Gibco BRL) using 10 ml/g tissue or 10 ml/10⁸ cells to isolate total RNA. Poly A RNA was purified from total RNA using Qiagen's Oligotex mRNA Mini and Midi kits. Total and mRNA were quantified by spectrophotometric analysis (O.D. 260/280 nm) and analyzed by gel electrophoresis.

Oligonucleotides:

The following HPLC purified oligonucleotides were used.

DPNCDN (cDNA synthesis primer): (SEQ ID NO: 29) 5′TTTTGATCAAGCTT₃₀3′ Adaptor 1: (SEQ ID NO: 30) 5′CTAATACGACTCACTATAGGGCTCGAGCGGCCGCCCGGGCAG3′ (SEQ ID NO: 31) 3′GGCCCGTCCTAG5′ Adaptor 2: (SEQ ID NO: 32) 5′GTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAG3′ (SEQ ID NO: 33) 3′CGGCTCCTAG5′ PCR primer 1: (SEQ ID NO: 34) 5′CTAATACGACTCACTATAGGGC3′ Nested primer (NP)1: (SEQ ID NO: 35) 5′TCGAGCGGCCGCCCGGGCAGGA3′ Nested primer (NP)2: (SEQ ID NO: 36) 5′AGCGTGGTCGCGGCCGAGGA3′

Suppression Subtractive Hybridization:

Suppression Subtractive Hybridization (SSH) was used to identify cDNAs corresponding to genes that may be differentially expressed in prostate cancer. The SSH reaction utilized cDNA from kidney cancer patient specimens. The gene 161P2F10B was derived from kidney cancer patient tissues minus normal kidney and a mixture of 9 normal tissues: stomach, skeletal muscle, lung, brain, liver, kidney, pancreas, small intestine and heart. The SSH DNA sequence (FIG. 1) was identified.

The cDNA derived from kidney cancer patient tissues was used as the source of the “driver” cDNA, while the cDNA from normal tissues was used as the source of the “tester” cDNA. Double stranded cDNAs corresponding to tester and driver cDNAs were synthesized from 2 μg of poly(A), RNA isolated from the relevant tissue, as described above, using CLONTECH's PCR-Select cDNA Subtraction Kit and 1 ng of oligonucleotide DPNCDN as primer. First- and second-strand synthesis were carried out as described in the Kit's user manual protocol (CLONTECH Protocol No. PT1117-1, Catalog No. K1804-1). The resulting cDNA was digested with Dpn II for 3 hrs at 37° C. Digested cDNA was extracted with phenol/chloroform (1:1) and ethanol precipitated.

Tester cDNA was generated by diluting 1 μl of Dpn II digested cDNA from the relevant tissue source (see above) (400 ng) in 5 μl of water. The diluted cDNA (2 μl 160 ng) was then ligated to 2 μl of Adaptor 1 and Adaptor 2 (10 μM), in separate ligation reactions, in a total volume of 10 μl at 16° C. overnight, using 400 u of T4 DNA ligase (CLONTECH). Ligation was terminated with 1 μl of 0.2 M EDTA and heating at 72° C. for 5 min.

The first hybridization was performed by adding 1.5 μl (600 ng) of driver cDNA to each of two tubes containing 1.5 μl (20 ng) Adaptor 1- and Adaptor 2-ligated tester cDNA. In a final volume of 4 μl, the samples were overlaid with mineral oil, denatured in an MJ Research thermal cycler at 98° C. for 1.5 minutes, and then were allowed to hybridize for 8 hrs at 68° C. The two hybridizations were then mixed together with an additional 1 μl of fresh denatured driver cDNA and were allowed to hybridize overnight at 68° C. The second hybridization was then diluted in 200 μl of 20 mM Hepes, pH 8.3, 50 mM NaCl, 0.2 rmM EDTA, heated at 70° C. for 7 min. and stored at −20° C.

PCR Amplification, Cloning and Sequencing of Gene Fragments Generated from SSH:

To amplify gene fragments resulting from SSH reactions, two PCR amplifications were performed. In the primary PCR reaction 1 μl of the diluted final hybridization mix was added to 1 μl of PCR primer 1 (10 μM), 0.5 μl dNTP mix (10 μM), 2.5 μl 10× reaction buffer (CLONTECH) and 0.5 μl 50× Advantage cDNA polymerase Mix (CLONTECH) in a final volume of 25 μl. PCR 1 was conducted using the following conditions: 75° C. for 5 min., 94° C. for 25 sec., then 27 cycles of 94° C. for 10 sec, 66° C. for 30 sec, 72° C. for 1.5 min. Five separate primary PCR reactions were performed for each experiment. The products were pooled and diluted 1:10 with water. For the secondary PCR reaction, 1 μl from the pooled and diluted primary PCR reaction was added to the same reaction mix as used for PCR 1, except that primers NP1 and NP2 (10 μM) were used instead of PCR primer 1. PCR 2 was performed using 10–12 cycles of 94° C. for 10 sec, 68° C. for 30 sec, and 72° C. for 1.5 minutes. The PCR products were analyzed using 2% agarose gel electrophoresis.

The PCR products were inserted into pCR2.1 using the T/A vector cloning kit (Invitrogen). Transformed E. coli were subjected to blue/white and ampicillin selection. White colonies were picked and arrayed into 96 well plates and were grown in liquid culture overnight. To identify inserts, PCR amplification was performed on 1 ml of bacterial culture using the conditions of PCR1 and NP1 and NP2 as primers. PCR products were analyzed using 2% agarose gel electrophoresis.

Bacterial clones were stored in 20% glycerol in a 96 well format. Plasmid DNA was prepared, sequenced, and subjected to nucleic acid homology searches of the GenBank, dBest, and NCI-CGAP databases.

RT-PCR Expression Analysis:

First strand cDNAs can be generated from 1 μg of mRNA with oligo (dT)12–18 priming using the Gibco-BRL Superscript Preamplification system. The manufacturer's protocol was used which included an incubation for 50 min at 42° C. with reverse transcriptase followed by RNAse H treatment at 37° C. for 20 min. After completing the reaction, the volume can be increased to 200 μl with water prior to normalization. First strand cDNAs from 16 different normal human tissues can be obtained from Clontech.

Normalization of the first strand cDNAs from multiple tissues was performed by using the primers 5′atatcgccgcgctcgtcgtcgacaa3′ (SEQ ID NO: 37) and 5′agccacacgcagctcattgtagaagg 3′ (SEQ ID NO: 38) to amplify β-actin. First strand cDNA (5 μl) were amplified in a total volume of 50 μl containing 0.4 μM primers, 0.2 μM each dNTPs, 1×PCR buffer (Clontech, 10 mM Tris-HCl, 1.5 mM MgCl₂, 50 mM KCl, pH8.3) and 1× Klentaq DNA polymerase (Clontech). Five μl of the PCR reaction can be removed at 18, 20, and 22 cycles and used for agarose gel electrophoresis. PCR was performed using an MJ Research thermal cycler under the following conditions: Initial denaturation can be at 94° C. for 15 sec, followed by a 18, 20, and 22 cycles of 94° C. for 15, 65° C. for 2 min, 72° C. for 5 sec. A final extension at 72° C. was carried out for 2 min. After agarose gel electrophoresis, the band intensities of the 283 bp β-actin bands from multiple tissues were compared by visual inspection. Dilution factors for the first strand cDNAs were calculated to result in equal β-actin band intensities in all tissues after 22 cycles of PCR. Three rounds of normalization can be required to achieve equal band intensities in all tissues after 22 cycles of PCR.

To determine expression levels of the 161P2F10B gene, 5 μl of normalized first strand cDNA were analyzed by PCR using 26, and 30 cycles of amplification. Semi-quantitative expression analysis can be achieved by comparing the PCR products at cycle numbers that give light band intensities.

A typical RT-PCR expression analysis is shown in FIG. 14. RT-PCR expression analysis was performed on first strand cDNAs generated using pools of tissues from multiple samples. The cDNAs were shown to be normalized using beta-actin PCR. Strong expression of 161P2F10B was observed in kidney cancer pool. Expression was also detected in VP1, prostate cancer xenograft pool, prostate cancer pool and colon cancer pool. Low expression was observed in VP2, lung cancer pool, ovary cancer pool, breast cancer pool, metastasis pool, pancreas cancer pool, and in the 2 different prostate cancer metastasis to lymph node.

Example 2 Isolation of Full Length 161P2F10B Encoding cDNA

To isolate genes that are involved in kidney cancer, an experiment was conducted using kidney cancer patient specimens. The gene 161P2F10B was derived from a subtraction consisting of kidney cancer specimens, minus normal kidney mixed with a cocktail of 9 normal tissues: stomach, skeletal muscle, lung, brain, liver, kidney, pancreas, small intestine and heart. The SSH DNA sequence (FIG. 1) was designated 161P2F10B. cDNA clone 161P2F10B was cloned from kidney cancer specimens (FIG. 2 and FIG. 3). 161P2F10B showed homology to the gene ENPP3. The amino acid alignment of 161P2F10B with ENPP3 is shown in FIG. 4 (also, see, e.g., Buhring, et al., Blood 97:3303–3305(2001)).

Example 3 Chromosomal Mapping of 161P2F10B

Chromosomal localization can implicate genes in disease pathogenesis. Several chromosome mapping approaches are available including fluorescent in situ hybridization (FISH), human/hamster radiation hybrid (RH) panels (Walter et al., 1994; Nature Genetics 7:22; Research Genetics, Huntsville Ala.), human-rodent somatic cell hybrid panels such as is available from the Coriell Institute (Camden, N.J.), and genomic viewers utilizing BLAST homologies to sequenced and mapped genomic clones (NCBI, Bethesda, Md.).

161P2F10B maps to chromosome 6q22, using 161P2F10B sequence and the NCBI BLAST tool.

Example 4 Expression Analysis of 161P2F10B

To compare expression of 161P2F10B in normal versus patient cancer tissues, RT-PCR experiment was performed using normal and patient cancer tissues (FIG. 14). First strand cDNA was generated from normal stomach, normal brain, normal heart, normal liver, normal skeletal muscle, normal testis, normal prostate, normal bladder, normal kidney, normal colon, normal lung, normal pancreas, and a pool of cancer specimens from prostate cancer patients, bladder cancer patients, kidney cancer patients, colon cancer patients, lung cancer patients, pancreas cancer patients, a pool of prostate cancer xenografts (LAPC-4AD, LAPC-4AI, LAPC-9AD and LAPC-9AI), and a pool of 2 patient prostate metastasis to lymph node. Normalization was performed by PCR using primers to actin. Semi-quantitative PCR, using primers to 161P2F10B, was performed at 26 and 30 cycles of amplification. Samples were run on an agarose gel, and PCR products were quantitated using the Alphalmager software. Results show strong expression in prostate cancer, bladder cancer, kidney cancer, colon cancer, lung cancer, pancreas cancer, bone cancer, lymphoma cancer, uterus cancer, compared to all normal tissues tested. Strong expression was also detected in the xenograft pool as well as the prostate cancer metastasis to lymph node specimens.

FIG. 15 & Table LIX shows expression of 161P2F10B in a panel of kidney cancer clear cell carcinoma (A), kidney cancer papillary carcinoma (B), and in uterus patient cancer specimens (C). First strand cDNA was prepared from the patient specimens. Normalization was performed by PCR using primers to actin. Semi-quantitative PCR, using primers to 161P2F10B, was performed at 26 and 30 cycles of amplification. Samples were run on an agarose gel, and PCR products were quantitated using the Adphalmager software. Expression was recorded as absent, low, medium or strong. Results show expression of 161P2F10B in 94.7% of clear cell renal carcinoma, 62.5% of papillary renal cell carcinoma, and in 61.5% of uterus cancer.

The restricted expression of 161P2F10B in normal tissues and the upregulation detected in kidney cancer, in kidney cancer metastasis, as well as in prostate, bladder, colon, lung, pancreas, bone, lymphoma, uterus, breast, and ovary cancers, suggest that 161P2F10B is a potential therapeutic target and a diagnostic marker for human cancers.

Example 5 Transcript Variants of 161P2F10B

Transcript variants are variants of mature mRNA from the same gene, which arise by alternative transcription or alternative splicing. Alternative transcripts are transcripts from the same gene but start transcription at different points. Splice variants are mRNA variants spliced differently from the same transcript. In eukaryotes, when a multi-exon gene is transcribed from genomic DNA, the initial RNA is spliced to produce functional mRNA, which has only exons and is used for translation into an amino acid sequence. Accordingly, a given gene can have zero to many alternative transcripts and each transcript can have zero to many splice variants. Each transcript variant has a unique exon makeup, and can have different coding and/or non-coding (5′ or 3′ end) portions, from the original transcript. Transcript variants can code for similar or different proteins with the same or a similar function or can encode proteins with different functions, and can be expressed in the same tissue at the same time, or in different tissues at the same time, or in the same tissue at different times, or in different tissues at different times. Proteins encoded by transcript variants can have similar or different cellular or extracellular localizations, e.g., secreted versus intracellular.

Transcript variants are identified by a variety of art-accepted methods. For example, alternative transcripts and splice variants are identified by full-length cloning experiment, or by use of full-length transcript and EST sequences. First, all human ESTs were grouped into clusters which show direct or indirect identity with each other. Second, ESTs in the same cluster were further grouped into sub-clusters and assembled into a consensus sequence. The original gene sequence is compared to the consensus sequence(s) or other full-length sequences. Each consensus sequence is a potential splice variant for that gene. Even when a variant is identified that is not a full-length clone, that portion of the variant is very useful for antigen generation and for further cloning of the full-length splice variant, using techniques known in the art.

Moreover, computer programs are available in the art that identify transcript variants based on genomic sequences. Genomic-based transcript variant identification programs include FgenesH (A. Salamov and V. Solovyev, “Ab initio gene finding in Drosophila genomic DNA,” Genome Research. 2000 April; 10(4):516–22); Grail (URL compbio.ornl.gov/Grail-bin/EmptyGrailForm) and Gen Scan (URL genes.mit.edu/GENSCAN.html). For a general discussion of splice variant identification protocols see., e.g., Southan, C., A genomic perspective on human proteases, FEBS Lett. 2001 Jun. 8; 498(2–3):214–8; de Souza, S. J., et al, Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags, Proc. Natl. Acad Sci USA. 200 Nov. 7; 97(23):12690–3.

To further confirm the parameters of a transcript variant, a variety of techniques are available in the art, such as full-length cloning, proteomic validation, PCR-based validation, and 5′ RACE validation, etc. (see e.g., Proteomic Validation: Brennan, S. O., et a., Albumin banks peninsula: a new termination variant characterized by electrospray mass spectrometry, Biochem Biophys Acta. 1999 Aug. 17; 1433(1–2):321–6; Ferranti P, et a., Differential splicing of pre-messenger RNA produces multiple forms of mature caprine alpha(sl)-casein, Eur J. Biochem. 1997 Oct. 31; 249(1):1–7. For PCR-based Validation: Wellmann S, et a., Specific reverse transcription-PCR quantification of vascular endothelial growth factor (VEGF) splice variants by LightCycler technology, Clin Chem. 2001 April; 47(4):654–60; Jia, H. P., et al, Discovery of new human beta-defensins using a genomics-based approach, Gene. Jan. 24, 2001; 263(1–2):211–8. For PCR-based and 5′ RACE Validation: Brigle, K. E., et al., Organization of the murine reduced folate carrier gene and identification of variant splice forms, Biochem Biophys Acta. Aug. 7, 1997; 1353(2): 191–8).

It is known in the art that genomic regions are modulated in cancers. When the genomic region to which a gene maps is modulated in a particular cancer, the alternative transcripts or splice variants of the gene are modulated as well. Disclosed herein is that 161P2F10B has a particular expression profile related to cancer. Alternative transcripts and splice variants of 161P2F10B may also be involved in cancers in the same or different issues, thus serving as tumor-associated markers/antigens.

Using the full-length gene and EST sequences, two transcript variants were identified, designated as 161P2F10B v.6 and v.7. Compared with 161P2F10B v.1, transcript variant 161P2F10B v.6 has extra 40 bases to the 5′ starting site of variant 161P2F10B v.1 transcript and has a different 3′ end portion, which is on the same chromosome as other exons in the current version of human genome. Variant 161P2F10B v.7 inserted 130 bases in between positions 121 and 122 of variant 161P2F10B v.1. Theoretically, each different combination of exons in spatial order, e.g. exons 2 and 3, is a potential splice variant. Due to the incorrect assembly of the chromosome region in the current version of human genome, the transcript structure cannot be derived computationally.

Tables LI through LVIII are set forth on a variant by variant bases. Tables LI and LV show the nucleotide sequence of the transcript variant. Tables LII and LVI show the alignment of the transcript variant with nucleic acid sequence of 161P2F10B v.1. Tables LIII and LVII lay out amino acid translation of the transcript variant for the identified reading frame orientation. Tables LIV and LVIII display alignments of the amino acid sequence encoded by the splice variant with that of 161P2F10B v.1.

Example 6 Single Nucleotide Polymorphisms of 161P2F10B

A Single Nucleotide Polymorphism (SNP) is a single base pair variation in a nucleotide sequence at a specific location. At any given point of the genome, there are four possible nucleotide base pairs: A/T, C/G, G/C and T/A. Genotype refers to the specific base pair sequence of one or more locations in the genome of an individual. Haplotype refers to the base pair sequence of more than one location on the same DNA molecule (or the same chromosome in higher organisms), often in the context of one gene or in the context of several tightly linked genes. SNPs that occur on a cDNA are called cSNPs. These cSNPs may change amino acids of the protein encoded by the gene and thus change the functions of the protein. Some SNPs cause inherited diseases; others contribute to quantitative variations in phenotype and reactions to environmental factors including diet and drugs among individuals. Therefore, SNPs and/or combinations of alleles (called haplotypes) have many applications, including diagnosis of inherited diseases, determination of drug reactions and dosage, identification of genes responsible for diseases, and analysis of the genetic relationship between individuals (P. Nowotny, J. M. Kwon and A. M. Goate, a “SNP analysis to dissect human traits,” Curr. Opin. Neurobiol. 2001 October; 11(5):637–641; M. Pirmohamed and B. K. Park, “Genetic susceptibility to adverse drug reactions,” Trends Pharmacol. Sci. 2001 June; 22(6):298–305; J. H. Riley, C. J. Allan, E. Lai and A. Roses, “The use of single nucleotide polymorphisms in the isolation of common disease genes,” Pharmacogenomics. 2000 February; 1(1):39–47; R. Judson, J. C. Stephens and A. Windemuth, “The predictive power of haplotypes in clinical response,” Pharmacogenomics. 2000 February; 1(1):15–26).

SNPs are identified by a variety of art-accepted methods (P. Bean, “The promising voyage of SNP target discovery,” Am. Clin. Lab. 2001 Oct–Nov; 20(9):18–20; K. M. Weiss, “In search of human variation,” Genome Res. 1998 July; 8(7):691–697; M. M. She, “Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies,” Clin. Chem. 2001 February; 47(2):164–172). For example, SNPs are identified by sequencing DNA fragments that show polymorphism by gel-based methods such as restriction fragment length polymorphism (RFLP) and denaturing gradient gel electrophoresis (DGGE). They can also be discovered by direct sequencing of DNA samples pooled from different individuals or by comparing sequences from different DNA samples. With the rapid accumulation of sequence data in public and private databases, one can discover SNPs by comparing sequences using computer programs (Z. Gu, L. Hillier and P. Y. Kwok, “Single nucleotide polymorphism hunting in cyberspace,” Hum. Mutat. 1998; 12(4):221–225). SNPs can be verified and genotype or haplotype of an individual can be determined by a variety of methods including direct sequencing and high throughput microarrays (P. Y. Kwok, “Methods for genotyping single nucleotide polymorphisms,” Annu. Rev. Genomics Hum. Genet. 2001; 2:235–258; M. Kokoris, K. Dix, K. Moynihan, J. Mathis, B. Erwin, P. Grass, B. Hines and A. Duesterhoeft, “High-throughput SNP genotyping with the Masscode system,” Mol. Diagn. 2000 December; 5(4):329–340). Using the methods described above, four SNPs were identified in the original transcript, 161P2F10B v.1, at positions 408 (A/G), 2502 (A/G), 2663 (A/C) and 3233 (A/C). The transcripts or proteins with alternative alleles were designated as variants 161P2F10B v.2, v.3, v.4, and v.5, respectively. FIG. 10 shows the schematic alignment of the SNP variants. FIG. 11 shows the schematic alignment of protein variants, corresponding to nucleotide variants. Nucleotide variants that code for the same amino acid sequence as variant I are not shown in FIG. 11. These alleles of the SNPs, though shown separately here, can occur in different combinations (haplotypes) and in any one of the transcript variants (such as 161P2F10B v.7) that contains the sequence context of the SNPS.

Example 7 Production of Recombinant 161P2F10B in Prokaryotic Systems

To express recombinant 161P2F10B in prokaryotic cells, the full or partial length 161P2F10B cDNA sequences can be cloned into any one of a variety of expression vectors known in the art. One or more of the following regions of 161P2F10B are expressed in these contructs, amino acids 1 to 875; or any 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more contiguous amino acids from 161P2F10B, variants, or analogs thereof.

A. In Vitro Transcription and Translation Constructs:

pCRII: To generate 161P2F10B sense and anti-sense RNA probes for RNA in situ investigations, pCRII constructs (Invitrogen, Carlsbad Calif.) are generated encoding either all or fragments of the 161P2F10B cDNA. The pCRII vector has Sp6 and T7 promoters flanking the insert to drive the transcription of 161P2F10B RNA for use as probes in RNA in situ hybridization experiments. These probes are used to analyze the cell and tissue expression of 161P2F10B at the RNA level. Transcribed 161P2F10B RNA representing the cDNA amino acid coding region of the 161P2F10B gene is used in in vitro translation systems such as the TnT™ Coupled Reticulolysate System (Promega, Corp., Madison, Wis.) to synthesize 161P2F10B protein.

B. Bacterial Constructs:

pGEX Constructs: To generate recombinant 161P2F10B proteins in bacteria that are fused to the Glutathione S-transferase (GST) protein, all or parts of the 161P2F10B cDNA protein coding sequence are fused to the GST gene by cloning into pGEX-6P-1 or any other GST-fusion vector of the pGEX family (Amersham Pharmacia Biotech, Piscataway, N.J.). These constructs allow controlled expression of recombinant 161P2F10B protein sequences with GST fused at the amino-terminus and a six histidine epitope (6× His) at the carboxyl-terminus. The GST and 6× His tags permit purification of the recombinant fusion protein from induced bacteria with the appropriate affinity matrix and allow recognition of the fusion protein with anti-GST and anti-His antibodies. The 6× His tag is generated by adding 6 histidine codons to the cloning primer at the 3′ end, e.g., of the open reading frame (ORF). A proteolytic cleavage site, such as the PreScission™ recognition site in pGEX-6P-1, may be employed such that it permits cleavage of the GST tag from 161P2F10B-related protein. The ampicillin resistance gene and pBR322 origin permits selection and maintenance of the pGEX plasmids in E coli.

pMAL Constructs: To generate, in bacteria, recombinant 161P2F10B proteins that are fused to maltose-binding protein (MBP), all or parts of the 161P2F10B cDNA protein coding sequence are fused to the MBP gene by cloning into the pMAL-c2X and pMAL-p2X vectors (New England Biolabs, Beverly, Mass.). These constructs allow controlled expression of recombinant 161P2F10B protein sequences with MBP fused at the amino-terminus and a 6× His epitope tag at the carboxyl-terminus. The MBP and 6× His tags permit purification of the recombinant protein from induced bacteria with the appropriate affinity matrix and allow recognition of the fusion protein with anti-MBP and anti-His antibodies. The 6× His epitope tag is generated by adding 6 histidine codons to the 3′ cloning primer. A Factor Xa recognition site permits cleavage of the pMAL tag from 161P2F10B. The pMAL-c2X and pMAL-p2X vectors are optimized to express the recombinant protein in the cytoplasm or periplasm respectively. Periplasm expression enhances folding of proteins with disulfide bonds.

pET Constructs: To express 161P2F10B in bacterial cells, all or parts of the 161P2F10B cDNA protein coding sequence are cloned into the pET family of vectors (Novagen, Madison, Wis.). These vectors allow tightly controlled expression of recombinant 161P2F10B protein in bacteria with and without fusion to proteins that enhance solubility, such as NusA and thioredoxin (Trx), and epitope tags, such as 6× His and S-Tag™ that aid purification and detection of the recombinant protein. For example, constructs are made utilizing pET NusA fusion system 43.1 such that regions of the 161P2F10B protein are expressed as amino-terminal fusions to NusA.

C. Yeast Constructs:

pESC Constructs: To express 161P2F10B in the yeast species Saccharomyces cerevisiae for generation of recombinant protein and functional studies, all or parts of the 161P2F108 cDNA protein coding sequence are cloned into the pESC family of vectors each of which contain 1 of 4 selectable markers, HIS3, TRP1, LEU2, and URA3 (Stratagene, La Jolla, Calif.). These vectors allow controlled expression from the same plasmid of up to 2 different genes or cloned sequences containing either Flag™ or Myc epitope tags in the same yeast cell. This system is useful to confirm protein-protein interactions of 161P2F10B. In addition, expression in yeast yields similar post-translational modifications, such as glycosylations and phosphorylations, that are found when expressed in eukaryotic cells.

pESP Constructs: To express 161P2F10B in the yeast species Saccharomyces pombe, all or parts of the 161P2F10B cDNA protein coding sequence are cloned into the pESP family of vectors. These vectors allow controlled high level of expression of a 161P2F10B protein sequence that is fused at either the amino terminus or at the carboxyl terminus to GST which aids purification of the recombinant protein. A Flag™ epitope tag allows detection of the recombinant protein with anti-Flag™ antibody.

Example 8 Production of Recombinant 161P2F10B in Higher Eukaryotic Systems

A. Mammalian Constructs:

To express recombinant 161P2F10B in eukaryotic cells, the full or partial length 161P2F10B cDNA sequences can be cloned into any one of a variety of expression vectors known in the art. One or more of the following regions of 161P2F10B are expressed in these constructs, amino acids 1 to 875; or any 8, 9, 10,11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more contiguous amino acids from 161P2F10B, variants, or analogs thereof.

The constructs were transfected into any one of a wide variety of mammalian cells such as 293T cells or kidney cancer cell lines. Transfected 293T cell lysates were probed with the anti-161P2F10B polyclonal serum and monoclonal antibodies, described herein.

PcDNA3.11MycHis Constructs: To express 161P2F10B in mammalian cells, the 161P2F10B ORF, or portions thereof, of 161P2F10B with a consensus Kozak translation initiation site were cloned into pcDNA3.1/MycHis Version A (Invitrogen, Carlsbad, Calif.). Protein expression is driven from the cytomegalovirus (CMV) promoter. The recombinant proteins have the myc epitope and 6× His epitope fused to the carboxyl-terminus. The pcDNA3.1/MycHis vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability, along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Neomycin resistance gene can be used, as it allows for selection of mammalian cells expressing the protein and the ampicillin resistance gene and ColE1 origin permits selection and maintenance of the plasmid in E. coli.

The pcDNA3.1/mycHis encoding 161P2F10B was transfected in 293T cells. Cells were harvested 24 hours later and analyzed showing cell surface expression of 161P2F10B driven from the pcDNA3.1/mycHis vector (FIG. 29).

pTaq5: The 161P2F10B ORF, or portions thereof, of 161P2F10B were cloned into pTag-5. This vector is similar to pAPtag but without the alkaline phosphatase fusion. This construct generates 161P2F10B protein with an amino-terminal IgGK signal sequence and myc and 6× His epitope tags at the carboxyl-terminus that facilitate detection and affinity purification. The resulting recombinant 161P2F10B protein was optimized for secretion into the media of transfected mammalian cells, and was used as immunogen or ligand to identify proteins such as ligands or receptors that interact with the 161P2F10B proteins. Protein expression is driven from the CMV promoter. The Zeocin resistance gene present in the vector allows for selection of mammalian cells expressing the protein, and the ampicillin resistance gene permits selection of the plasmid in E coli. FIGS. 31 and 32 show expression and enzymatic activity of the soluble pTag5 expressing various growth factors by the transformed cells. The degree of growth factor or serum dependence of transformed host cells

PsecFc: The 161P2F10B ORF, or portions thereof, of 161P2F10B were cloned into psecFc. The psecFc vector was assembled by cloning the human immunoglobulin G1 (IgG) Fc (hinge, CH2, CH3 regions) into pSecTag2 (Invitrogen, California). This construct generates an IgG1 Fc fusion at the amino-terminus of the 161P2F10B proteins. 161P2F10B fusions utilizing the murine IgG1 Fc region was also generated and expressed. The resulting recombinant 161P2F10B proteins are optimized for secretion into the media of transfected mammalian cells, and can be used as immunogens or to identify proteins such as ligands or receptors that interact with the 161P2F10B protein. Protein expression is driven from the CMV promoter. The hygromycin resistance gene present in the vector allows for selection of mammalian cells that express the recombinant protein, and the ampicillin resistance gene permits selection of the plasmid in E coli.

pSRα Constructs: To generate mammalian cell lines that express 161P2F10B constitutively, 1611P2F10B ORF, or portions thereof, of 161P2F10B are cloned into pSRa constructs. Amphotropic and ecotropic retroviruses were generated by transfection of pSRα constructs into the 293T-10A1 packaging line or co-transfection of pSRα and a helper plasmid (containing deleted packaging sequences) into the 293 cells. The retrovirus is used to infect a variety of mammalian cell lines, resulting in the integration of the cloned gene, 161P2F10B, into the host cell-lines. Protein expression is driven from a long terminal repeat (LTR). The Neomycin resistance gene present in the vector allows for selection of mammalian cells that express the protein, and the ampicillin resistance gene and ColE1 origin permit selection and maintenance of the plasmid in E. coli. The retroviral vectors were thereafter used for infection and generation of various cell lines using, for example, NIH 3T3, 293 Rat-1 cells or kidney cancer cell lines such as Caki and 769 cells. FIGS. 16 and 30 show cell surface expression of 161P2F10B driven from the pSRa construct in Caki and NIH3T3 cells respectively.

Additional pSRα constructs were generated encoding 3 different mutants of 161P2F10B. The first mutant is D80E, converted the D amino acid residue of the RGD domain at position 80 into E. The other mutants are mutants of the active site of 161P2F10B, converting the T205 amino acid residue at position 205 into either A (T205A), or S (T205S). The 3 mutant pSRa constructs were transfected into a variety of mammalian cell lines such as 293T cells and CaKi kidney cancer cells. Expression was confirmed using anti-161P2F10B monoclonal antibody and phosphodiesterase enzyme activity was tested (FIG. 30).

pcDNA4/HisMax Constructs: To express 161P2F10B in mammalian cells, the 161P2F10B ORF, or portions thereof, of 161P2F10B are cloned into pcDNA4/HisMax Version A (Invitrogen, Carlsbad, Calif.). Protein expression is driven from the cytomegalovirus (CMV) promoter and the SP16 translational enhancer. The recombinant protein has XpressT and six histidine (6× His) epitopes fused to the amino-terminus. The pcDNA4/HisMax vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Zeocin resistance gene allows for selection of mammalian cells expressing the protein and the ampicillin resistance gene and ColE1 origin permits selection and maintenance of the plasmid in E. coli.

pcDNA3.1/CTGFβ-TOPO Construct: To express 161P2F10B in mammalian cells and to allow detection of the recombinant proteins using fluorescence, the 161P2F10B ORF, or portions thereof, of 161P2F10B with a consensus Kozak translation initiation site are cloned into pcDNA3.1/CT-GFP-TOPO (Invitrogen, CA). Protein expression is driven from the cytomegalovirus (CMV) promoter. The recombinant proteins have the Green Fluorescent Protein (GFP) fused to the carboxyl-terminus facilitating non-invasive, in vivo detection and cell biology studies. The pcDNA3.1/CT-GFP-TOPO vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Neomycin resistance gene allows for selection of mammalian cells that express the protein, and the ampicillin resistance gene and ColE1 origin permits selection and maintenance of the plasmid in E coli. Additional constructs with an amino-terminal GFP fusion are made in pcDNA3.1/NT-GFP-TOPO spanning the entire length of the 161P2F10B proteins.

PAPtag: The 161P2F10B ORF, or portions thereof, of 161P2F10B are cloned into pAPtag-5 (GenHunter Corp. Nashville, Tenn.). This construct generates an alkaline phosphatase fusion at the carboxyl-terminus of the 161P2F10B proteins while fusing the IgGK signal sequence to the amino-terminus. Constructs are also generated in which alkaline phosphatase with an amino-terminal IgGK signal sequence is fused to the amino-terminus of 161P2F10B proteins. The resulting recombinant 161P2F10B proteins are optimized for secretion into the media of transfected mammalian cells and can be used to identify proteins such as ligands or receptors that interact with the 161P2F10B proteins. Protein expression is driven from the CMV promoter and the recombinant proteins also contain myc and 6× His epitopes fused at the carboxyl-terminus that facilitates detection and purification. The Zeocin resistance gene present in the vector allows for selection of mammalian cells expressing the recombinant protein and the ampicillin resistance gene permits selection of the plasmid in E. coli.

Additional Viral Vectors: Additional constructs are made for viral-mediated delivery and expression of 161P2F10B. High virus titer leading to high-level expression of 161P2F10B is achieved in viral delivery systems such as adenoviral vectors and herpes amplicon vectors. The 161P2F10B coding sequences or fragments thereof are amplified by PCR and subcloned into the AdEasy shuttle vector (Stratagene). Recombination and virus packaging are performed according to the manufacturer's instructions to generate adenoviral vectors. Alternatively, 161P2F10B coding sequences or fragments thereof are cloned into the HSV-1 vector (Imgenex) to generate herpes viral vectors. The viral vectors are thereafter used for infection of various cell lines such as PC3, NIH 3T3, 293 or rat-1 cells.

Regulated Expression Systems: To control expression of 161P2F10B in mammalian cells, coding sequences of 161P2F10B, or portions thereof, are cloned into regulated mammalian expression systems such as the T-Rex System (Invitrogen), the GeneSwitch System (Invitrogen) and the tightly-regulated Ecdysone System (Sratagene). These systems allow the study of the temporal and concentration dependent effects of recombinant 161P2F10B. These vectors are thereafter used to control expression of 161P2F10B in various cell lines such as PC3, NIH 3T3, 293 or rat-1 cells.

B. Baculovirus Expression Systems

To generate recombinant 161P2F10B proteins in a Baculovirus expression system, 161P2F10B ORF, or portions thereof, are cloned into the Baculovirus transfer vector pBlueBac 4.5 (Invitrogen), which provides a His-tag at the N-terminus. Specifically, pBlueBac-161P2F10B is co-transfected with helper plasmid pBac-N-Blue (Invitrogen) into SF9 (Spodoptera frugiperda) insect cells to generate recombinant Baculovirus (see Invitrogen instruction manual for details). Baculovirus is then collected from cell supernatant and purified by plaque assay.

Recombinant 161P2F10B protein is then generated by infection of HighFive insect cells (Invitrogen) with purified Baculovirus. Recombinant 161P2F10B protein can be detected using anti-161P2F10B or anti-His-tag antibody. 161P2F10B protein can be purified and used in various cell-based assays or as immunogen to generate polyclonal and monoclonal antibodies specific for 161P2F10B.

Example 9 Antigenicity Profiles and Secondary Structure

FIG. 5, FIG. 6, FIG. 7, FIG. 8, and FIG. 9 depict graphically five amino acid profiles of the 161P2F10B amino acid sequence, each assessment available by accessing the ProtScale website on the ExPasy molecular biology server.

These profiles: FIG. 5, Hydrophilicity, (Hopp T. P., Woods K. R., 1981. Proc. Natl. Acad. Sci. U.S.A. 78:3824–3828); FIG. 6, Hydropathicity, (Kyte J., Doolittle R. F., 1982. J. Mol. Biol. 157:105–132); FIG. 7, Percentage Accessible Residues (Janin J., 1979 Nature 277:491–492); FIG. 8, Average Flexibility, (Bhaskaran R., and Ponnuswamy P. K., 1988. Int. J. Pept. Protein Res. 32:242–255); FIG. 9, Beta-turn (Deleage, G., Roux B. 1987 Protein Engineering 1:289–294); and optionally others available in the art, such as on the ProtScale website, were used to identify antigenic regions of the 161P2F10B protein. Each of the above amino acid profiles of 161P2F10B were generated using the following ProtScale parameters for analysis: 1) A window size of 9; 2) 100% weight of the window edges compared to the window center; and, 3) amino acid profile values normalized to lie between 0 and 1.

Hydrophilicity (FIG. 5), Hydropathicity (FIG. 6) and Percentage Accessible Residues (FIG. 7) profiles were used to determine stretches of hydrophilic amino acids (i.e., values greater than 0.5 on the Hydrophilicity and Percentage Accessible Residues profile, and values less than 0.5 on the Hydropathicity profile). Such regions are likely to be exposed to the aqueous environment, be present on the surface of the protein, and thus available for immune recognition, such as by antibodies.

Average Flexibility (FIG. 8) and Beta-turn (FIG. 9) profiles determine stretches of amino acids (i.e., values greater than 0.5 on the Beta-turn profile and the Average Flexibility profile) that are not constrained in secondary structures such as beta sheets and alpha helices. Such regions are also more likely to be exposed on the protein and thus accessible to immune recognition, such as by antibodies.

Antigenic sequences of the 161P2F10B protein indicated, e.g., by the profiles set forth in FIG. 5, FIG. 6, FIG. 7, FIG. 8, and/or FIG. 9 are used to prepare immunogens, either peptides or nucleic acids that encode them, to generate therapeutic and diagnostic anti-161P2F10B antibodies. The immunogen can be any 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or more than 50 contiguous amino acids, or the corresponding nucleic acids that encode them, from the 161P2F10B protein. In particular, peptide immunogens of the invention can comprise, a peptide region of at least 5 amino acids of FIG. 2 in any whole number increment up to 875 that includes an amino acid position having a value greater than 0.5 in the Hydrophilicity profile of FIG. 5; a peptide region of at least 5 amino acids of FIG. 2 in any whole number increment up to 875 that includes an amino acid position having a value less than 0.5 in the Hydropathicity profile of FIG. 6; a peptide region of at least 5 amino acids of FIG. 2 in any whole number increment up to 875 that includes an amino acid position having a value greater than 0.5 in the Percent Accessible Residues profile of FIG. 7; a peptide region of at least 5 amino acids of FIG. 2 in any whole number increment up to 875 that includes an amino acid position having a value greater than 0.5 in the Average Flexibility profile on FIG. 8; and, a peptide region of at least 5 amino acids of FIG. 2 in any whole number increment up to 875 that includes an amino acid position having a value greater than 0.5 in the Beta-turn profile of FIG. 9. Peptide immunogens of the invention can also comprise nucleic acids that encode any of the forgoing.

All immunogens of the invention, peptide or nucleic acid, can be embodied in human unit dose form, or comprised by a composition that includes a pharmaceutical excipient compatible with human physiology.

The secondary structure of 161P2F10B, namely the predicted presence and location of alpha helices, extended strands, and random coils, is predicted from the primary amino acid sequence using the HNN—Hierarchical Neural Network method, accessed from the ExPasy molecular biology server. The analysis indicates that 161P2F10B is composed 31.31% alpha helix, 11.31% extended strand, and 57.37% random coil (FIG. 19A).

Analysis for the potential presence of transmembrane domains in 161P2F10B was carried out using a variety of transmembrane prediction algorithms accessed from the ExPasy molecular biology server. The programs predict the presence of 1 transmembrane domain in 161P2F10B, consistent with that of a Type II cell surface protein. Shown graphically in FIG. 19 are the results of analysis using the TMpred (FIG. 19B) and TMHMM (FIG. 19C) prediction programs depicting the location of the transmembrane domain.

Example 10 Generation of 161P2F10B Polyclonal Antibodies

Polyclonal antibodies can be raised in a mammal, for example, by one or more injections of an immunizing agent and, if desired, an adjuvant. Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperitoneal injections. In addition to immunizing with the full length 161P2F10B protein, computer algorithms are employed in design of immunogens that, based on amino acid sequence analysis contain characteristics of being antigenic and available for recognition by the immune system of the immunized host (see the Example entitled “Antigenicity Profiles”). Such regions would be predicted to be hydrophilic, flexible, in beta-turn conformations, and be exposed on the surface of the protein (see, e.g., FIG. 5, FIG. 6, FIG. 7, FIG. 8, or FIG. 9 for amino acid profiles that indicate such regions of 161P2F10B).

For example, 161P2F10B recombinant bacterial fusion proteins or peptides containing hydrophilic, flexible, beta-turn regions of the 161P2F10B, in which numerous regions are found in the predicted extracellular domain coded by amino acids 45–870, are used as antigens to generate polyclonal antibodies in New Zealand White rabbits. For example, such regions include, but are not limited to, amino acids 43–93, 100–134, 211–246,467–492, 500–517, and amino acids 810–870. In addition, recombinant proteins are made that encode the whole extracellular domain, amino acids 45–870, or halves of the domain, such as amino acids 45–450 and amino acids 451–870. Antigens are also created encoding the Somatomedin-B-like domain (amino acids 53–133), the catalytic domain (amino acids 158–538), and the nuclease like domain (amino acids 609–875) of 161P2F10B (Bollen et. al., 2000. Crit. Rev. Biochem. Mol. Biol., 35: 393–432), in order to generate antibodies specific to these regions. Ideally antibodies are raised to non-conserved regions of these domains such that they do not crossreact with other homologous nucleotide pyrophosphatases/phosphodiesterases. It is useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include, but are not limited to, keyhole limpet hemocyanin (KLH), serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. In one embodiment, a peptide encoding amino acids 500–517 of 161P2F10B is conjugated to KLH and used to immunize the rabbit. Alternatively the immunizing agent may include all or portions of the 161P2F10B protein, analogs or fusion proteins thereof. For example, the 161P2F10B amino acid sequence can be fused using recombinant DNA techniques to any one of a variety of fusion protein partners that are well known in the art, such as glutathione-S-transferase (GST) and HIS tagged fusion proteins. Such fusion proteins are purified from induced bacteria using the appropriate affinity matrix.

In one embodiment, a GST-fusion protein encoding amino acids 45–875 is produced and purified and used as immunogen. Other recombinant bacterial fusion proteins that may be employed include maltose binding protein, LacZ, thioredoxin, NusA, or an immunoglobulin constant region (see the section entitled Production of 161P2F10B in Prokaryotic Systems' and Current Protocols In Molecular Biology, Volume 2, Unit 16, Frederick M. Ausubul et al. eds., 1995; Linsley, P.S., Brady, W., Urnes, M., Grosmaire, L., Damle, N., and Ledbetter, L.(1991) J. Exp. Med. 174, 561–566).

In addition to bacterial derived fusion proteins, mammalian expressed protein antigens are also used. These antigens are expressed from mammalian expression vectors such as the Tag5 and Fc-fusion vectors (see the section entitled Production of Recombinant 161P2F10B in “Eukaryotic Systems”), and retain post-translational modifications such as glycosylations found in native protein. In one embodiment, amino acids 45–875 is cloned into the Tag5 mammalian secretion vector. The recombinant protein is purified by metal chelate chromatography from tissue culture supernatants of 293T cells stably expressing the recombinant vector. The purified Tag5 161P2F10B protein is then used as immunogen.

During the immunization protocol, it is useful to mix or emulsify the antigen in adjuvants that enhance the immune response of the host animal. Examples of adjuvants include, but are not limited to, complete Freund's adjuvant (CFA) and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate).

In a typical protocol, rabbits are initially immunized subcutaneously with up to 200 μg, typically 100–200 μg, of fusion protein or peptide conjugated to KLH mixed in complete Freund's adjuvant (CFA). Rabbits are then injected subcutaneously every two weeks with up to 200 μg, typically 100–200 μg, of the immunogen in incomplete Freund's adjuvant (IFA). Test bleeds are taken approximately 7–10 days following each immunization and used to monitor the titer of the antiserum by ELISA.

To test reactivity and specificity of immune serum, such as the rabbit serum derived from immunization with Tag5 161P2F10B encoding amino acids 58–538, the full-length 161P2F10B cDNA is cloned into pcDNA 3.1 myc-his expression vector (Invitrogen, see the Example entitled Production of Recombinant 161P2F10B in “Eukaryotic Systems”). After transfection of the constructs into 293T cells, cell lysates are probed with the anti-161P2F10B serum and with anti-His antibody (Santa Cruz Biotechnologies, Santa Cruz, Calif.) to determine specific reactivity to denatured 161P2F10B protein using the Western blot technique. Immunoprecipitation and flow cytometric analyses of 293T and other recombinant 161P2F10B-expressing cells determine recognition of native protein by the antiserum. In addition, Western blot, immunoprecipitation, fluorescent microscopy, and flow cytometric techniques using cells that endogenously express 161P2F10B are carried out to test specificity.

The anti-serum from the Tag5 161P2F10B immunized rabbit is affinity purified by passage over a column composed of the Tag5 antigen covalently coupled to Affigel matrix (BioRad, Hercules, Calif.). The serum is then further purified by protein G affinity chromatography to isolate the IgG fraction. Serum from rabbits immunized with fusion proteins, such as GST and MBP fusion proteins, are purified by depletion of antibodies reactive to the fusion partner sequence by passage over an affinity column containing the fusion partner either alone or in the context of an irrelevant fusion protein. Sera from other His-tagged antigens and peptide immunized rabbits as well as fusion partner depleted sera are affinity purified by passage over a column matrix composed of the original protein immunogen or free peptide.

Example 11 Generation of 161P2F10B Monoclonal Antibodies (mAbs)

The use of agents to identify the presence of 161P2F10Bin biopsy specimens or to neutralize the effect of 161P2F10B has a beneficial effect in diagnosis, prognoosis, prophylaxis and/or therapy. One particularly useful class of anti 161P2F10B agents is antibodies, in particular monoclonal antibodies (Mabs) to 161P2F10B. Anti 161P2F10B Abs, such as Mabs, are generated that react with the epitopes of the 161P2F10B protein such that they either indicate it's presence, disrupt or modulate it's biological function (for example those that would disrupt the interaction with ligands or proteins that mediate or are involved in it's biological activity) or are able to carry a toxin to the cell which is expressing 161P2F10B.

The term anti 161P2F10B antibody as used herein is to be understood to cover antibodies to any epitope of the 161P2F10B gene product. Diagnostic Mabs, e.g. those used for imaging or immunocytochemistry, comprise those that specifically bind epitopes of 161P2F10B protein and thus demonstrate its presence. Therapeutic Mabs include those that are useful for diagnosis but also comprise those that specifically bind epitopes of 161P2F10B exposed on the cell surface and thus are useful to modulate growth and survival of cells expressing 161P2F10B by disrupting the function of a cell expressing 161P2F10B and/or disrupting the interaction of cells expressing 161P2F10B and the ligand for 161P2F10B.

Preferred antibodies which form one aspect of the invention include but are not limited to antibodies entitled X41(4)6, X41(3)17, X41(3)50, X41(3)15, X41(3)29 and X41(3)37 secreted by a hybridoma deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, Va. 20110-2209 USA) on Nov. 7, 2002 and assigned as Patent Deposit Designation No. PTA-4794, Patent Deposit Designation No. PTA-4792, Patent Deposit Designation No. PTA-4793, Patent Deposit Designation No. PTA-4791, Patent Deposit Designation No. PTA-4791, and Patent Deposit Designation No. PTA-4791 (respectively); and derivatives thereof, the production of which is described herein.

Pathological conditions which are characterized by the presence of 161P2F10B expression include, but are not restricted to, neoplasms of tissues such as those listed in Table I. One aspect of the invention provides a method of detecting the presence of 161P2F10B. A further aspect of the invention provides a method of treatment of conditions characterized by the presence of 161P2F10B, comprising administering an effective amount of an anti 161P2F10B antibody. The administration of anti-161 P2F10B antibody is particularly advantageous in the treatment of conditions characterized by the presence of 161P2F10B.

The antibodies against 161P2F10B for use according to the invention can be from any species, and can belong to any immunoglobulin class. Thus, for example, the anti 161P2F10B antibody for use according to the invention can be an immunoglobulin G (IgG), Immunoglobulin M (IgM), immunoglobulin A (IgA), Immunoglobulin E (IgE) or immunoglobulin D (IgD).

The anti 161P2F10B antibody can be from an animal, for example mammaliam or avian origin, and can be for example of murine, rat or human origin. The antibody can be a whole immunoglobulin, or a fragment thereof, for example a fragment derived by proteolytic cleavage of a whole antibody, such as F(ab′)2, Fab′ or Fab fragments or fragments obtained by recombinant DNA techniques, for example Fv fragments.

Particularly useful antibodies for use according to the invention include humanized or fully human anti 161P2F10B antibodies and fragments thereof. These antibodies are produced by any suitable procedure including, but not restricted to, mammalian cell and bacterial cell fermentation systems.

The anti 161P2F10B Mabs are prepared by immunological techniques employing 161P2F10B antigens. Thus, for example, any suitable host can be injected (immunized) with a suitable reagent which makes 161P2F10B available as an immunogen. Examples of reagents which make 161P2F10B available as an immunogen are purified protein (e.g. the whole extra-cellular domain (ecd) or fragments there of), peptides designed using the full length protein as a template (e.g peptides encompassing the catalytic domain), DNA vectors encoding all or truncated fragments of the ecd, recombinant cells expressing 161P2F10B (e.g. Rat-1, Mouse 3T3, Mouse 300.19, and mouse NSO), Cell lines with endogenous 161P2F10B expression (e.g. human UT-7) or xenografts (i.e. patient derived clear cell and papillary xenografts).

Immune cells, for example splenocytes or lymphocytes, are recovered from the immunized host and immortalized, using for example the method of Kohler et al, Eur. J. Immunol 6, 511 (1976), or their immunoglobulin genes can be isolated and transferred to an appropriate DNA vector for expression in an appropriate cell type. The resulting cells, generated by either technique, will be selected to obtain a single genetic line producing a single unique type of antibody more commonly known as a monoclonal antibody. Antibody fragments can be produced using techniques such as enzymatic digestion of whole antibodies e.g. with pepsin (Parham, J. Immunol 131:2895 (1983)) or papain (Lamoyi and Nisonoff, J. Immunol Meth. 56:235 (1983)), or by recombinant DNA techniques.

Suitable hosts for the production of Mab's to 161P2F10B include mice, rats, hamsters and rabbits. For example, mice are immunized with a number of different reagents which make 161P2F10B available as a source of antigenic material (immunogen). The route and timing if the immunizations will depend on the source and/or embodiment of the immunogen. Sources of immunogen for 161P2F10B include, but are not restricted to, peptide, protein, fusion protein, DNA, RNA, cells or cell membranes as detailed above. These can be used separately as immunogens or in combination to produce a specific immune reaction to 161P2F10B. The use and application of these various immunogens is described fully in the accompanying examples.

Example 12 HLA Class I and Class II Binding Assays

HLA class I and class II binding assays using purified HLA molecules are performed in accordance with disclosed protocols (e.g., PCT publications WO 94/20127 and WO 94/03205; Sidney et al., Current Protocols in Immunology 18.3.1 (1998); Sidney, et al., J. Immunol. 154:247 (1995); Sette, et al., Mol. Immunol. 31:813 (1994)). Briefly, purified MHC molecules (5 to 500 nM) are incubated with various unlabeled peptide inhibitors and 1–10 nM ¹²⁵I-radiolabeled probe peptides as described. Following incubation, MHC-peptide complexes are separated from free peptide by gel filtration and the fraction of peptide bound is determined. Typically, in preliminary experiments, each MHC preparation is titered in the presence of fixed amounts of radiolabeled peptides to determine the concentration of HLA molecules necessary to bind 10–20% of the total radioactivity. All subsequent inhibition and direct binding assays are performed using these HLA concentrations.

Since under these conditions [label]<[HLA] and IC₅₀≧[HLA], the measured IC₅₀ values are reasonable approximations of the true K_(D) values. Peptide inhibitors are typically tested at concentrations ranging from 120 μg/ml to 1.2 ng/ml, and are tested in two to four completely independent experiments. To allow comparison of the data obtained in different experiments, a relative binding figure is calculated for each peptide by dividing the IC₅₀ of a positive control for inhibition by the IC₅₀ for each tested peptide (typically unlabeled versions of the radiolabeled probe peptide). For database purposes, and inter-experiment comparisons, relative binding values are compiled. These values can subsequently be converted back into IC₅₀ nM values by dividing the IC₅₀ nM of the positive controls for inhibition by the relative binding of the peptide of interest. This method of data compilation is accurate and consistent for comparing peptides that have been tested on different days, or with different lots of purified MHC.

Binding assays as outlined above may be used to analyze HLA supermotif and/or HLA motif-bearing peptides (see Table IV).

Example 13 Identification of HLA Supermotif- and Motif-Bearing CTL Candidate Epitopes

HLA vaccine compositions of the invention can include multiple epitopes. The multiple epitopes can comprise multiple HLA supermotifs or motifs to achieve broad population coverage. This example illustrates the identification and confirmation of supermotif- and motif-bearing epitopes for the inclusion in such a vaccine composition. Calculation of population coverage is performed using the strategy described below.

Computer Searches and Algorithms for Identification of Supermotif and/or Motif-Bearing Epitomes

The searches performed to identify the motif-bearing peptide sequences in the Example entitled “Antigenicity Profiles” and Tables VIII–XXI and XXII–XLIX employ the protein sequence data from the gene product of 161P2F10B set forth in FIGS. 2 and 3, the specific search peptides used to generate the tables are listed in Table VII.

Computer searches for epitopes bearing HLA Class I or Class II supermotifs or motifs are performed as follows. All translated 161P2F10B protein sequences are analyzed using a text string search software program to identify potential peptide sequences containing appropriate HLA binding motifs; such programs are readily produced in accordance with information in the art in view of known motif/supermotif disclosures. Furthermore, such calculations can be made mentally.

Identified A2-, A3-, and DR-supermotif sequences are scored using polynomial algorithms to predict their capacity to bind to specific HLA-Class I or Class II molecules. These polynomial algorithms account for the impact of different amino acids at different positions, and are essentially based on the premise that the overall affinity (or AG) of peptide-HLA molecule interactions can be approximated as a linear polynomial function of the type: “ΔG”=a _(1i) ×a _(2i) ×a _(3i) . . . ×a _(ni)

where a_(ji) is a coefficient which represents the effect of the presence of a given amino acid (j) at a given position (i) along the sequence of a peptide of n amino acids. The crucial assumption of this method is that the effects at each position are essentially independent of each other (i.e., independent binding of individual side-chains). When residue j occurs at position i in the peptide, it is assumed to contribute a constant amount j_(i) to the free energy of binding of the peptide irrespective of the sequence of the rest of the peptide.

The method of derivation of specific algorithm coefficients has been described in Gulukota et al., J. Mol. Biol. 267:1258–126, 1997; (see also Sidney et al., Human Immunol. 45:79–93, 1996; and Southwood et al., J. Immunol. 160:3363–3373, 1998). Briefly, for all i positions, anchor and non-anchor alike, the geometric mean of the average relative binding (ARB) of all peptides carrying j is calculated relative to the remainder of the group, and used as the estimate of j_(i). For Class II peptides, if multiple alignments are possible, only the highest scoring alignment is utilized, following an iterative procedure. To calculate an algorithm score of a given peptide in a test set, the ARB values corresponding to the sequence of the peptide are multiplied. If this product exceeds a chosen threshold, the peptide is predicted to bind. Appropriate thresholds are chosen as a function of the degree of stringency of prediction desired.

Selection of HLA-A2 Supertype Cross-reactive Peptides

Protein sequences from 161P2F10B are scanned utilizing motif identification software, to identify 8-, 9-10- and 11-mer sequences containing the HLA-A2-supermotif main anchor specificity. Typically, these sequences are then scored using the protocol described above and the peptides corresponding to the positive-scoring sequences are synthesized and tested for their capacity to bind purified HLA-A*0201 molecules in vitro (HLA-A*0201 is considered a prototype A2 supertype molecule).

These peptides are then tested for the capacity to bind to additional A2-supertype molecules (A*0202, A*0203, A*0206, and A*6802). Peptides that bind to at least three of the five A2-supertype alleles tested are typically deemed A2-supertype cross-reactive binders. Preferred peptides bind at an affinity equal to or less than 500 nM to three or more HLA-A2 supertype molecules.

Selection of HLA-A3 Supermotif-bearing Epitopes

The 161P2F10B protein sequence(s) scanned above is also examined for the presence of peptides with the HLA-A3-supermotif primary anchors. Peptides corresponding to the HLA A3 supermotif-bearing sequences are then synthesized and tested for binding to HLA-A*0301 and HLA-A*1101 molecules, the molecules encoded by the two most prevalent A3-supertype alleles. The peptides that bind at least one of the two alleles with binding affinities of ≦500 nM, often ≦200 nM, are then tested for binding cross-reactvity to the other common A3-supertype alleles (e.g., A*3101, A*3301, and A*6801) to identify those that can bind at least three of the five HLA-A3-supertype molecules tested.

Selection of HLA-B7 Supermotif Bearing Epitopes

The 161P2F10B protein(s) scanned above is also analyzed for the presence of 8-, 9–10-, or 11-mer peptides with the HLA-B7-supermotif. Corresponding peptides are synthesized and tested for binding to HLA-B*0702, the molecule encoded by the most common B7-supertype allele (i.e., the prototype B7 supertype allele). Peptides binding B*0702 with IC₅₀ of ≦500 nM are identified using standard methods. These peptides are then tested for binding to other common B7-supertype molecules (e.g., B*3501, B*5101, B*5301, and B*5401). Peptides capable of binding to three or more of the five B7-supertype alleles tested are thereby identified.

Selection of A1 and A24 Motif-Bearing Epitopes

To further increase population coverage, HLA-A1 and -A24 epitopes can also be incorporated into vaccine compositions. An analysis of the 161P2F10B protein can also be performed to identify HLA-A1- and A24-motif-containing sequences.

High affinity and/or cross-reactive binding epitopes that bear other motif and/or supermotifs are identified using analogous methodology.

Example 14 Confirmation of Immunogenicity

Cross-reactive candidate CTL A2-supermotif-bearing peptides that are identified as described herein are selected to confirm in vitro immunogenicity. Confirmation is performed using the following methodology:

Target Cell Lines for Cellular Screening:

The 0.221A2.1 cell line, produced by transferring the HLA-A2.1 gene into the HLA-A, -B, -C null mutant human B-lymphoblastoid cell line 721.221, is used as the peptide-loaded target to measure activity of HLA-A2.1-restricted CTL. This cell line is grown in RPMI-1640 medium supplemented with antibiotics, sodium pyruvate, nonessential amino acids and 10% (v/v) heat inactivated FCS. Cells that express an antigen of interest, or transfectants comprising the gene encoding the antigen of interest, can be used as target cells to confirm the ability of peptide-specific CTLs to recognize endogenous antigen.

Primary CTL Induction Cultures:

Generation of Dendritic Cells (DC): PBMCs are thawed in RPMI with 30 μg/ml DNAse, washed twice and resuspended in complete medium (RPMI-1640 plus 5% AB human serum, non-essential amino acids, sodium pyruvate, L-glutamine and penicillin/streptomycin). The monocytes are purified by plating 10×10⁶ PBMC/well in a 6-well plate. After 2 hours at 37° C., the non-adherent cells are removed by gently shaking the plates and aspirating the supernatants. The wells are washed a total of three times with 3 ml RPMI to remove most of the non-adherent and loosely adherent cells. Three ml of complete medium containing 50 ng/ml of GM-CSF and 1,000 U/ml of IL-4 are then added to each well. TNFα is added to the DCs on day 6 at 75 ng/ml and the cells are used for CTL induction cultures on day 7.

Induction of CTL with DC and Peptide. CD8+ T-cells are isolated by positive selection with Dynal immunomagnetic beads (Dynabeads® M-450) and the detacha-bead(D reagent. Typically about 200–250×10⁶ PBMC are processed to obtain 24×10⁶ CD8, T-cells (enough for a 48-well plate culture). Briefly, the PBMCs are thawed in RPMI with 30 μg/ml DNAse, washed once with PBS containing 1% human AB serum and resuspended in PBS/1% AB serum at a concentration of 20×10⁶cells/ml. The magnetic beads are washed 3 times with PBS/AB serum, added to the cells (140 μl beads/20×10⁶ cells) and incubated for 1 hour at 4° C. with continuous mixing. The beads and cells are washed 4× with PBS/AB serum to remove the nonadherent cells and resuspended at 100×10⁶ cells/ml (based on the original cell number) in PBS/AB serum containing 100 μl/ml detacha-bead® reagent and 30 μg/ml DNAse. The mixture is incubated for 1 hour at room temperature with continuous mixing. The beads are washed again with PBS/AB/DNAse to collect the CD8+ T-cells. The DC are collected and centrifuged at 1300 rpm for 5–7 minutes, washed once with PBS with 1% BSA, counted and pulsed with 40 μg/ml of peptide at a cell concentration of 1–2×10⁶/ml in the presence of 3 μg/ml β₂-microglobulin for 4 hours at 20° C. The DC are then irradiated (4,200 rads), washed 1 time with medium and counted again.

Setting up induction cultures: 0.25 ml cytokine-generated DC (at 1×10⁵ cells/ml) are co-cultured with 0.25 ml of CD8+ T-cells (at 2×10⁶ cell/ml) in each well of a 48-well plate in the presence of 10 ng/ml of IL-7. Recombinant human IL-10 is added the next day at a final concentration of 10 ng/ml and rhuman IL-2 is added 48 hours later at 10 IU/ml.

Restimulation of the induction cultures with peptide-pulsed adherent cells: Seven and fourteen days after the primary induction, the cells are restimulated with peptide-pulsed adherent cells. The PBMCs are thawed and washed twice with RPMI and DNAse. The cells are resuspended at 5×10⁶ cells/ml and irradiated at ˜4200 rads. The PBMCs are plated at 2×10⁶ in 0.5 ml complete medium per well and incubated for 2 hours at 37° C. The plates are washed twice with RPMI by tapping the plate gently to remove the nonadherent cells and the adherent cells pulsed with 10 μg/ml of peptide in the presence of 3 μg/ml β₂ microglobulin in 0.25 ml RPMI/5% AB per well for 2 hours at 37° C. Peptide solution from each well is aspirated and the wells are washed once with RPMI. Most of the media is aspirated from the induction cultures (CD8+ cells) and brought to 0.5 ml with fresh media. The cells are then transferred to the wells containing the peptide-pulsed adherent cells. Twenty four hours later recombinant human IL-10 is added at a final concentration of 10 ng/ml and recombinant human IL2 is added the next day and again 2–3 days later at 50 lU/ml (Tsai et al., Critical Reviews in Immunology 18(1–2):65–75, 1998). Seven days later, the cultures are assayed for CTL activity in a ⁵¹Cr release assay. In some experiments the cultures are assayed for peptide-specific recognition in the in situ IFNγ ELISA at the time of the second restimulation followed by assay of endogenous recognition 7 days later. After expansion, activity is measured in both assays for a side-by-side comparison.

Measurement of CTL Lytic Activity by ⁵¹Cr Release.

Seven days after the second restimulation, cytotoxicity is determined in a standard (5 hr) ⁵¹Cr release assay by assaying individual wells at a single E:T. Peptide-pulsed targets are prepared by incubating the cells with 10 μg/ml peptide overnight at 37° C.

Adherent target cells are removed from culture flasks with trypsin-EDTA. Target cells are labeled with 200 μCi of ⁵¹Cr sodium chromate (Dupont, Wilmington, Del.) for 1 hour at 37° C. Labeled target cells are resuspended at 10⁶ per ml and diluted 1:10 with K562 cells at a concentration of 3.3×10⁶/ml (an NK-sensitive erythroblastoma cell line used to reduce non-specific lysis). Target cells (100 μl) and effectors (100 μl) are plated in 96 well round-bottom plates and incubated for 5 hours at 37° C. At that time, 100 μl of supernatant are collected from each well and percent lysis is determined according to the formula: [(cpm of the test sample-cpm of the spontaneous ⁵¹Cr release sample)/(cpm of the maximal ⁵¹Cr release sample-cpm of the spontaneous ⁵¹Cr release sample)]×100.

Maximum and spontaneous release are determined by incubating the labeled targets with 1% Triton X-100 and media alone, respectively. A positive culture is defined as one in which the specific lysis (sample-background) is 10% or higher in the case of individual wells and is 15% or more at the two highest E:T ratios when expanded cultures are assayed.

In Situ Measurement of Human IFNY Production as an Indicator of Peptide-Specific and Endogenous Recognition

Immulon 2 plates are coated with mouse anti-human IFNγ monoclonal antibody (4 μg/ml 0.1M NaHCO₃, pH8.2) overnight at 4° C. The plates are washed with Ca²⁺, Mg²⁺ free PBS/0.05% Tween 20 and blocked with PBS/10% FCS for two hours, after which the CTLs (100 μl/well) and targets (100 μl/well) are added to each well, leaving empty wells for the standards and blanks (which received media only). The target cells, either peptide-pulsed or endogenous targets, are used at a concentration of 1×10⁶ cells/ml. The plates are incubated for 48 hours at 37° C. with 5% CO2.

Recombinant human IFN-gamma is added to the standard wells starting at 400 μg or 1200 μg/100 microliter/well and the plate incubated for two hours at 37° C. The plates are washed and 100 μl of biotinylated mouse anti-human IFN-gamma monoclonal antibody (2 microgram/ml in PBS/3% FCS/0.05% Tween 20) are added and incubated for 2 hours at room temperature. After washing again, 100 microliter HRP-streptavidin (1:4000) are added and the plates incubated for one hour at room temperature. The plates are then washed 6× with wash buffer, 100 microliter/well developing solution (TMB 1:1) are added, and the plates allowed to develop for 5–15 minutes. The reaction is stopped with 50 microliter/well 1M H₃PO₄ and read at OD450. A culture is considered positive if it measured at least 50 pg of IFN-gamma/well above background and is twice the background level of expression.

CTL Expansion.

Those cultures that demonstrate specific lytic activity against peptide-pulsed targets and/or tumor targets are expanded over a two week period with anti-CD3. Briefly, 5×10⁴ CD8+ cells are added to a T25 flask containing the following: 1×10⁶ irradiated (4,200 rad) PBMC (autologous or allogeneic) per ml, 2×10⁵ irradiated (8,000 rad) EBV-transformed cells per ml, and OKT3 (anti-CD3) at 30 ng per ml in RPMI-1640 containing 10% (v/v) human AB serum, non-essential amino acids, sodium pyruvate, 25 μM 2-mercaptoethanol, L-glutamine and penicillin/streptomycin. Recombinant human IL2 is added 24 hours later at a final concentration of 200 lU/ml and every three days thereafter with fresh media at 501U/ml. The cells are split if the cell concentration exceeds 1×10⁶/ml and the cultures are assayed between days 13 and 15 at E:T ratios of 30, 10, 3 and 1:1 in the ⁵¹Cr release assay or at 1×10⁶/ml in the in situ IFNγ assay using the same targets as before the expansion.

Cultures are expanded in the absence of anti-CD3⁺ as follows. Those cultures that demonstrate specific lytic activity against peptide and endogenous targets are selected and 5×10⁴ CD8+ cells are added to a T25 flask containing the following: 1×10⁶ autologous PBMC per ml which have been peptide-pulsed with 10 μg/ml peptide for two hours at 37° C. and irradiated (4,200 rad); 2×10⁵ irradiated (8,000 rad) EBV-transformed cells per ml RPMI-1640 containing 10%(v/v) human AB serum, non-essential AA, sodium pyruvate, 25 mM 2-ME, L-glutamine and gentamicin.

Immunogenicity of A2 Supermotif-Bearing Peptides

A2-supermotif cross-reactive binding peptides are tested in the cellular assay for the ability to induce peptide-specific CTL in normal individuals. In this analysis, a peptide is typically considered to be an epitope if it induces peptide-specific CTLs in at least individuals, and preferably, also recognizes the endogenously expressed peptide.

Immunogenicity can also be confirmed using PBMCs isolated from patients bearing a tumor that expresses 161P2F10B. Briefly, PBMCs are isolated from patients, re-stimulated with peptide-pulsed monocytes and assayed for the ability to recognize peptide-pulsed target cells as well as transfected cells endogenously expressing the antigen.

Evaluation of A*03/A11 Immunogenicity

HLA-A3 supermotif-bearing cross-reactive binding peptides are also evaluated for immunogenicity using methodology analogous for that used to evaluate the immunogenicity of the HLA-A2 supermotif peptides.

Evaluation of B7 Immunogenicity

Immunogenicity screening of the B7-supertype cross-reactive binding peptides identified as set forth herein are confirmed in a manner analogous to the confirmation of A2- and A3-supermotif-bearing peptides.

Peptides bearing other supermotifs/motifs, e.g., HLA-A1, HLA-A24 etc. are also confirmed using similar methodology

Example 15 Implementation of the Extended Supermotif to Improve the Binding Capacity of Native Epitopes by Creating Analogs

HLA motifs and supermotifs (comprising primary and/or secondary residues) are useful in the identification and preparation of highly cross-reactive native peptides, as demonstrated herein. Moreover, the definition of HLA motifs and supermotifs also allows one to engineer highly cross-reactive epitopes by identifying residues within a native peptide sequence which can be analoged to confer upon the peptide certain characteristics, e.g. greater cross-reactivity within the group of HLA molecules that comprise a supertype, and/or greater binding affinity for some or all of those HLA molecules. Examples of analoging peptides to exhibit modulated binding affinity are set forth in this example.

Analoging at Primary Anchor Residues

Peptide engineering strategies are implemented to further increase the cross-reactivity of the epitopes. For example, the main anchors of A2-supermotif-bearing peptides are altered, for example, to introduce a preferred L, I, V, or M at position 2, and I or V at the C-terminus.

To analyze the cross-reactivity of the analog peptides, each engineered analog is initially tested for binding to the prototype A2 supertype allele A*0201, then, if A*0201 binding capacity is maintained, for A2-supertype cross-reactivity.

Alternatively, a peptide is confirmed as binding one or all supertype members and then analoged to modulate binding affinity to any one (or more) of the supertype members to add population coverage.

The selection of analogs for immunogenicity in a cellular screening analysis is typically further restricted by the capacity of the parent wild type (WT) peptide to bind at least weakly, i.e., bind at an IC₅₀ of 500 nM or less, to three of more A2 supertype alleles. The rationale for this requirement is that the WT peptides must be present endogenously in sufficient quantity to be biologically relevant. Analoged peptides have been shown to have increased immunogenicity and cross-reactivity by T cells specific for the parent epitope (see, e.g., Parkhurst et al., J. Immunol. 157:2539, 1996; and Pogue et al., Proc. Natl. Acad. Sci. USA 92:8166,1995).

In the cellular screening of these peptide analogs, it is important to confirm that analog-specific CTLs are also able to recognize the wild-type peptide and, when possible, target cells that endogenously express the epitope.

Analoging of HLA-A3 and B7-supermotif-bearing peptides Analogs of HLA-A3 supermotif-bearing epitopes are generated using strategies similar to those employed in analoging HLA-A2 supermotif-bearing peptides. For example, peptides binding to ⅗ of the A3-supertype molecules are engineered at primary anchor residues to possess a preferred residue (V, S, M, or A) at position 2.

The analog peptides are then tested for the ability to bind A*03 and A*11 (prototype A3 supertype alleles). Those peptides that demonstrate ≦500 nM binding capacity are then confirmed as having A3-supertype cross-reactivity.

Similarly to the A2- and A3-motif bearing peptides, peptides binding 3 or more B7-supertype alleles can be improved, where possible, to achieve increased cross-reactive binding or greater binding affinity or binding half life. B7 supermotif-bearing peptides are, for example, engineered to possess a preferred residue (V, I, L, or F) at the C-terminal primary anchor position, as demonstrated by Sidney et al. (J. Immunol. 157:3480–3490, 1996).

Analoging at primary anchor residues of other motif and/or supermotif-bearing epitopes is performed in a like manner.

The analog peptides are then be confirmed for immunogenicity, typically in a cellular screening assay. Again, it is generally important to demonstrate that analog-specific CTLs are also able to recognize the wild-type peptide and, when possible, targets that endogenously express the epitope.

Analoging at Secondary Anchor Residues

Moreover, HLA supermotifs are of value in engineering highly cross-reactive peptides and/or peptides that bind HLA molecules with increased affinity by identifying particular residues at secondary anchor positions that are associated with such properties. For example, the binding capacity of a B7 supermotif-bearing peptide with an F residue at position 1 is analyzed. The peptide is then analoged to, for example, substitute L for F at position 1. The analoged peptide is evaluated for increased binding affinity, binding half life and/or increased cross-reactivity. Such a procedure identifies analoged peptides with enhanced properties.

Engineered analogs with sufficiently improved binding capacity or cross-reactivity can also be tested for immunogenicity in HLA-B7-transgenic mice, following for example, IFA immunization or lipopeptide immunization. Analoged peptides are additionally tested for the ability to stimulate a recall response using PBMC from patients with 161P2F10B-expressing tumors.

Other Analoging Strategies

Another form of peptide analoging, unrelated to anchor positions, involves the substitution of a cysteine with α-amino butyric acid. Due to its chemical nature, cysteine has the propensity to form disulfide bridges and sufficiently alter the peptide structurally so as to reduce binding capacity. Substitution of x-amino butyric acid for cysteine not only alleviates this problem, but has been shown to improve binding and crossbinding capabilities in some instances (see, e.g., the review by Selte et al., In: Persistent Viral Infections, Eds. R. Ahmed and 1. Chen, John Wiley & Sons, England, 1999).

Thus, by the use of single amino acid substitutions, the binding properties and/or cross-reactivity of peptide ligands for HLA supertype molecules can be modulated.

Example 16 Identification and Confirmation of 161P2F10B-Derived Sequences with HLA-DR Binding Motifs

Peptide epitopes bearing an HLA class II supermotif or motif are identified and confirmed as outlined below using methodology similar to that described for HLA Class I peptides.

Selection of HLA-DR-Supermotif-Bearing Epitopes.

To identify 161P2F10B-derived, HLA class II HTL epitopes, a 161P2F10B antigen is analyzed for the presence of sequences bearing an HLA-DR-motif or supermotif. Specifically, 15-mer sequences are selected comprising a DR-supermotif, comprising a 9-mer core, and three-residue N- and C-terminal flanking regions (15 amino acids total).

Protocols for predicting peptide binding to DR molecules have been developed (Southwood et al., J. Immunol. 160:3363–3373, 1998). These protocols, specific for individual DR molecules, allow the scoring, and ranking, of 9amer core regions. Each protocol not only scores peptide sequences for the presence of DR-supermotif primary anchors (i.e., at position 1 and position 6) within a 9-mer core, but additionally evaluates sequences for the presence of secondary anchors. Using allele-specific selection tables (see, e.g., Southwood et al., ibid), it has been found that these protocols efficiently select peptide sequences with a high probability of binding a particular DR molecule. Additionally, it has been found that performing these protocols in tandem, specifically those for DR1, DR4w4, and DR7, can efficiently select DR cross-reactive peptides.

The 161P2F10B-derived peptides identified above are tested for their binding capacity for various common HLA-DR molecules. All peptides are initially tested for binding to the DR molecules in the primary panel: DR1, DR4w4, and DR7. Peptides binding at least two of these three DR molecules are then tested for binding to DR2w2 P1, DR2w202, DR6w19, and DR9 molecules in secondary assays. Finally, peptides binding at least two of the four secondary panel DR molecules, and thus cumulatively at least four of seven different DR molecules, are screened for binding to DR4w15, DR5w11, and DR8w2 molecules in tertiary assays. Peptides binding at least seven of the ten DR molecules comprising the primary, secondary, and tertiary screening assays are considered cross-reactive DR binders. 161P2F10B-derived peptides found to bind common HLA-DR alleles are of particular interest.

Selection of DR3 Motif Peptides

Because HLA-DR3 is an allele that is prevalent in Caucasian, Black, and Hispanic populations, DR3 binding capacity is a relevant criterion in the selection of HTL epitopes. Thus, peptides shown to be candidates may also be assayed for their DR3 binding capacity. However, in view of the binding specificity of the DR3 motif, peptides binding only to DR3 can also be considered as candidates for inclusion in a vaccine formulation.

To efficiently identify peptides that bind DR3, target 161P2F10B antigens are analyzed for sequences carrying one of the two DR3-specific binding motifs reported by Geluk et al. (J. Immunol. 152:5742–5748, 1994). The corresponding peptides are then synthesized and confirmed as having the ability to bind DR3 with an affinity of 1 μM or better, i.e., less than 1 μM. Peptides are found that meet this binding criterion and qualify as HLA class II high affinity binders.

DR3 binding epitopes identified in this manner are included in vaccine compositions with DR supermotif-bearing peptide epitopes.

Similarly to the case of HLA class I motif-bearing peptides, the class II motif-bearing peptides are analoged to improve affinity or cross-reactivity. For example, aspartic acid at position 4 of the 9-mer core sequence is an optimal residue for DR3 binding, and substitution for that residue often improves DR 3 binding.

Example 17 Immunogenicity of 161P2F10B-Derived HTL Epitopes

This example determines immunogenic DR supermotif- and DR3 motif-bearing epitopes among those identified using the methodology set forth herein.

Immunogenicity of HTL epitopes are confirmed in a manner analogous to the determination of immunogenicity of CTL epitopes, by assessing the ability to stimulate HTL responses and/or by using appropriate transgenic mouse models. Immunogenicity is determined by screening for: 1.) in vitro primary induction using normal PBMC or 2.) recall responses from patients who have 161P2F10B-expressing tumors.

Example 18 Calculation of Phenotypic Frequencies of HLA-supertypes in Various Ethnic Backgrounds to Determine Breadth of Population Coverage

This example illustrates the assessment of the breadth of population coverage of a vaccine composition comprised of multiple epitopes comprising multiple supermotifs and/or motifs.

In order to analyze population coverage, gene frequencies of HLA alleles are determined. Gene frequencies for each HLA allele are calculated from antigen or allele frequencies utilizing the binomial distribution formulae gf=1-(SQRT(1-af) (see, e.g., Sidney et al., Human Immunol. 45:79–93, 1996). To obtain overall phenotypic frequencies, cumulative gene frequencies are calculated, and the cumulative antigen frequencies derived by the use of the inverse formula [af=1-(1-Cgf)2].

Where frequency data is not available at the level of DNA typing, correspondence to the serologically defined antigen frequencies is assumed. To obtain total potential supertype population coverage no linkage disequilibrium is assumed, and only alleles confirmed to belong to each of the supertypes are included (minimal estimates). Estimates of total potential coverage achieved by inter-loci combinations are made by adding to the A coverage the proportion of the non-A covered population that could be expected to be covered by the B alleles considered (e.g., total=A+B*(1-A)). Confirmed members of the A3-like supertype are A3, Al1, A31, A*3301, and A*6801. Although the A3-like supertype may also include A34, A66, and A*7401, these alleles were not included in overall frequency calculations. Likewise, confirmed members of the A2-like supertype family are A*0201, A*0202, A*0203, A*0204, A*0205, A*0206, A*0207, A*6802, and A*6901. Finally, the B7-like supertype-confirmed alleles are: B7, B*3501–03, B51, B*5301, B*5401, B*5501–2, B*5601, B*6701, and B*7801 (potentially also B*1401, B*3504–06, B*4201, and B*5602).

Population coverage achieved by combining the A2-, A3- and B7-supertypes is approximately 86% in five major ethnic groups. Coverage may be extended by including peptides bearing the A1 and A24 motifs. On average, A1 is present in 12% and A24 in 29% of the population across five different major ethnic groups (Caucasian, North American Black, Chinese, Japanese, and Hispanic). Together, these alleles are represented with an average frequency of 39% in these same ethnic populations. The total coverage across the major ethnicities when A1 and A24 are combined with the coverage of the A2-, A3- and B7-supertype alleles is >95%, see, e.g., Table IV (G). An analogous approach can be used to estimate population coverage achieved with combinations of class II motif-bearing epitopes.

Immunogenicity studies in humans (e.g., Bertoni et al., J. Clin. Invest. 100:503, 1997; Doolan et al., Immunity 7:97, 1997; and Threlkeld et al., J. Immunol. 159:1648, 1997) have shown that highly cross-reactive binding peptides are almost always recognized as epitopes. The use of highly cross-reactive binding peptides is an important selection criterion in identifying candidate epitopes for inclusion in a vaccine that is immunogenic in a diverse population.

With a sufficient number of epitopes (as disclosed herein and from the art), an average population coverage is predicted to be greater than 95% in each of five major ethnic populations. The game theory Monte Carlo simulation analysis, which is known in the art (see e.g., Osborne, M. J. and Rubinstein, A. “A course in game theory” MIT Press, 1994), can be used to estimate what percentage of the individuals in a population comprised of the Caucasian, North American Black, Japanese, Chinese, and Hispanic ethnic groups would recognize the vaccine epitopes described herein. A preferred percentage is 90%. A more preferred percentage is 95%.

Example 19 CTL Recognition of Endogenously Processed Antigens After Priming

This example confirms that CTL induced by native or analoged peptide epitopes identified and selected as described herein recognize endogenously synthesized, i.e., native antigens.

Effector cells isolated from transgenic mice that are immunized with peptide epitopes, for example HLA-A2 supermotif-bearing epitopes, are re-stimulated in vitro using peptide-coated stimulator cells. Six days later, effector cells are assayed for cytotoxicity and the cell lines that contain peptide-specific cytotoxic activity are further re-stimulated. An additional six days later, these cell lines are tested for cytotoxic activity on ⁵¹Cr labeled Jurkat-A2.1/K^(b) target cells in the absence or presence of peptide, and also tested on ⁵¹Cr labeled target cells bearing the endogenously synthesized antigen, i.e. cells that are stably transfected with 161P2F10B expression vectors.

The results demonstrate that CTL lines obtained from animals primed with peptide epitope recognize endogenously synthesized 161P2F10B antigen. The choice of transgenic mouse model to be used for such an analysis depends upon the epitope(s) that are being evaluated. In addition to HLA-A*0201/K^(b) transgenic mice, several other transgenic mouse models including mice with human A11, which may also be used to evaluate A3 epitopes, and B7 alleles have been characterized and others (e.g., transgenic mice for HLA-A1 and A24) are being developed. HLA-DR1 and HLA-DR3 mouse models have also been developed, which may be used to evaluate HTL epitopes.

Example 20 Activity of CTL-HTL Conjugated Epitopes in Transgenic Mice

This example illustrates the induction of CTLs and HTLs in transgenic mice, by use of a 161P2F10B-derived CTL and HTL peptide vaccine compositions. The vaccine composition used herein comprise peptides to be administered to a patient with a 161P2F10B-expressing tumor. The peptide composition can comprise multiple CTL and/or HTL epitopes. The epitopes are identified using methodology as described herein. This example also illustrates that enhanced immunogenicity can be achieved by inclusion of one or more HTL epitopes in a CTL vaccine composition; such a peptide composition can comprise an HTL epitope conjugated to a CTL epitope. The CTL epitope can be one that binds to multiple HLA family members at an affinity of 500 nM or less, or analogs of that epitope. The peptides may be lipidated, if desired.

Immunization procedures: Immunization of transgenic mice is performed as described (Alexander et al., J. Immunol. 159:4753–4761, 1997). For example, A2/K^(b) mice, which are transgenic for the human HLA A2.1 allele and are used to confirm the immunogenicity of HLA-A*0201 motif- or HLA-A2 supermotif-bearing epitopes, and are primed subcutaneously (base of the tail) with a 0.1 ml of peptide in Incomplete Freund's Adjuvant, or if the peptide composition is a lipidated CTL/HTL conjugate, in DMSO/saline, or if the peptide composition is a polypeptide, in PBS or Incomplete Freund's Adjuvant. Seven days after priming, splenocytes obtained from these animals are restimulated with syngenic irradiated LPS-activated lymphoblasts coated with peptide.

Cell lines: Target cells for peptide-specific cytotoxicity assays are Jurkat cells transfected with the HLA-A2.1/K^(b) chimeric gene (e.g., Vitiello et al., J. Exp. Med. 173:1007, 1991)

In vitro CTL activation: One week after priming, spleen cells (30×10⁶ cells/flask) are co-cultured at 37° C. with syngeneic, irradiated (3000 rads), peptide coated lymphoblasts (10×10⁶ cells/flask) in 10 ml of culture medium/T25 flask. After six days, effector cells are harvested and assayed for cytotoxic activity.

Assay for cytotoxic activity: Target cells (1.0 to 1.5×10⁶) are incubated at 37° C. in the presence of 200 μl of ⁵¹Cr. After 60 minutes, cells are washed three times and resuspended in R10 medium. Peptide is added where required at a concentration of 1 μg/ml. For the assay, 10⁴ ⁵¹Cr-labeled target cells are added to different concentrations of effector cells (final volume of 200 μl) in U-bottom 96-well plates. After a six hour incubation period at 37° C., a 0.1 ml aliquot of supernatant is removed from each well and radioactivity is determined in a Micromedic automatic gamma counter. The percent specific lysis is determined by the formula: percent specific release=100×(experimental release−spontaneous release)/(maximum release−spontaneous release). To facilitate comparison between separate CTL assays run under the same conditions, % ⁵¹Cr release data is expressed as lytic units/10⁶ cells. One lytic unit is arbitrarily defined as the number of effector cells required to achieve 30% lysis of 10,000 target cells in a six hour ⁵¹Cr release assay. To obtain specific lytic units/10⁶, the lytic units/10⁶ obtained in the absence of peptide is subtracted from the lytic units/10⁶ obtained in the presence of peptide. For example, if 30% ⁵¹Cr release is obtained at the effector (E): target (T) ratio of 50:1 (i.e., 5×10⁵ effector cells for 10,000 targets) in the absence of peptide and 5:1 (i.e., 5×10⁴ effector cells for 10,000 targets) in the presence of peptide, the specific lytic units would be: [(1/50,000)−(1/500,000)]×10⁶=18 LU.

The results are analyzed to assess the magnitude of the CTL responses of animals injected with the immunogenic CTL/HTL conjugate vaccine preparation and are compared to the magnitude of the CTL response achieved using, for example, CTL epitopes as outlined above in the Example entitled “Confirmation of Immunogenicity.” Analyses similar to this may be performed to confirm the immunogenicity of peptide conjugates containing multiple CTL epitopes and/or multiple HTL epitopes. In accordance with these procedures, it is found that a CTL response is induced, and concomitantly that an HTL response is induced upon administration of such compositions.

Example 21 Selection of CTL and HTL Epitopes for Inclusion in a 161P2F10B-Specific Vaccine

This example illustrates a procedure for selecting peptide epitopes for vaccine compositions of the invention. The peptides in the composition can be in the form of a nucleic acid sequence, either single or one or more sequences (i.e., minigene) that encodes peptide(s), or can be single and/or polyepitopic peptides.

The following principles are utilized when selecting a plurality of epitopes for inclusion in a vaccine composition. Each of the following principles is balanced in order to make the selection.

Epitopes are selected which, upon administration, mimic immune responses that are correlated with 161P2F10B clearance. The number of epitopes used depends on observations of patients who spontaneously clear 161P2F10B. For example, if it has been observed that patients who spontaneously clear 161P2F10B-expressing cells generate an immune response to at least three (3) epitopes from 161P2F10B antigen, then at least three epitopes should be included for HLA class I. A similar rationale is used to determine HLA class II epitopes.

Epitopes are often selected that have a binding affinity of an IC₅₀ of 500 nM or less for an HLA class I molecule, or for class II, an IC₅₀ of 1000 nM or less; or HLA Class I peptides with high binding scores from the BIMAS web site.

In order to achieve broad coverage of the vaccine through out a diverse population, sufficient supermotif bearing peptides, or a sufficient array of allele-specific motif bearing peptides, are selected to give broad population coverage. In one embodiment, epitopes are selected to provide at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art, can be employed to assess breadth, or redundancy, of population coverage.

When creating polyepitopic compositions, or a minigene that encodes same, it is typically desirable to generate the smallest peptide possible that encompasses the epitopes of interest. The principles employed are similar, if not the same, as those employed when selecting a peptide comprising nested epitopes. For example, a protein sequence for the vaccine composition is selected because it has maximal number of epitopes contained within the sequence, i.e., it has a high concentration of epitopes. Epitopes may be nested or overlapping (i.e., frame shifted relative to one another). For example, with overlapping epitopes, two 9-mer epitopes and one 10-mer epitope can be present in a 10 amino acid peptide. Each epitope can be exposed and bound by an HLA molecule upon administration of such a peptide. A multi-epitopic, peptide can be generated synthetically, recombinantly, or via cleavage from the native source. Alternatively, an analog can be made of this native sequence, whereby one or more of the epitopes comprise substitutions that alter the cross-reactivity and/or binding affinity properties of the polyepitopic peptide. Such a vaccine composition is administered for therapeutic or prophylactic purposes. This embodiment provides for the possibility that an as yet undiscovered aspect of immune system processing will apply to the native nested sequence and thereby facilitate the production of therapeutic or prophylactic immune response-inducing vaccine compositions. Additionally such an embodiment provides for the possibility of motif-bearing epitopes for an HLA makeup that is presently unknown. Furthermore, this embodiment (absent the creating of any analogs) directs the immune response to multiple peptide sequences that are actually present in 161P2F10B, thus avoiding the need to evaluate any junctional epitopes. Lastly, the embodiment provides an economy of scale when producing nucleic acid vaccine compositions. Related to this embodiment, computer programs can be derived in accordance with principles in the art, which identify in a target sequence, the greatest number of epitopes per sequence length.

A vaccine composition comprised of selected peptides, when administered, is safe, efficacious, and elicits an immune response similar in magnitude to an immune response that controls or clears cells that bear or overexpress 161P2F10B.

Example 22 Construction of “Minigene” Multi-Epitope DNA Plasmids

This example discusses the construction of a minigene expression plasmid Minigene plasmids may, of course, contain various configurations of B cell, CTL and/or HTL epitopes or epitope analogs as described herein.

A minigene expression plasmid typically includes multiple CTL and HTL peptide epitopes. In the present example, HLA-A2, -A3, -B7 supermotif-bearing peptide epitopes and HLA-A1 and -A24 motif-bearing peptide epitopes are used in conjunction with DR supermotif-bearing epitopes and/or DR3 epitopes. HLA class I supermotif or motif-bearing peptide epitopes derived 161P2F10B, are selected such that multiple supermotifs/motifs are represented to ensure broad population coverage. Similarly, HLA class II epitopes are selected from 161P2F10B to provide broad population coverage, i.e. both HLA DR-1–4–7 supermotif-bearing epitopes and HLA DR-3 motif-bearing epitopes are selected for inclusion in the minigene construct. The selected CTL and HTL epitopes are then incorporated into a minigene for expression in an expression vector.

Such a construct may additionally include sequences that direct the HTL epitopes to the endoplasmic reticulum. For example, the II protein may be fused to one or more HTL epitopes as described in the art, wherein the CLIP sequence of the II protein is removed and replaced with an HLA class II epitope sequence so that HLA class II epitope is directed to the endoplasmic reticulum, where the epitope binds to an HLA class II molecules.

This example illustrates the methods to be used for construction of a minigene-bearing expression plasmid. Other expression vectors that may be used for minigene compositions are available and known to those of skill in the art.

The minigene DNA plasmid of this example contains a consensus Kozak sequence and a consensus murine kappa Ig-light chain signal sequence followed by CTL and/or HTL epitopes selected in accordance with principles disclosed herein. The sequence encodes an open reading frame fused to the Myc and His antibody epitope tag coded for by the pcDNA 3.1 Myc-His vector.

Overlapping oligonucleotides that can, for example, average about 70 nucleotides in length with 15 nucleotide overlaps, are synthesized and HPLC-purified. The oligonucleotides encode the selected peptide epitopes as well as appropriate linker nucleotides, Kozak sequence, and signal sequence. The final multiepitope minigene is assembled by extending the overlapping oligonucleotides in three sets of reactions using PCR. A Perkin/Elmer 9600 PCR machine is used and a total of 30 cycles are performed using the following conditions: 95° C. for 15 sec, annealing temperature (5° below the lowest calculated Tm of each primer pair) for 30 sec, and 72° C. for 1 min.

For example, a minigene is prepared as follows. For a first PCR reaction, 5 μg of each of two oligonucleotides are annealed and extended: In an example using eight oligonucleotides, i.e., four pairs of primers, oligonucleotides 1+2, 3+4, 5+6, and 7+8 are combined in 100 μl reactions containing Pfu polymerase buffer (1×=10 mM KCL, 10 mM (NH4)₂SO₄, 20 mM Tris-chloride, pH 8.75, 2 mM MgSO₄, 0.1% Triton X-100, 100 μg/ml BSA), 0.25 mM each dNTP, and 2.5 U of Pfu polymerase. The full-length dimer products are gel-purified, and two reactions containing the product of 1+2 and 3+4, and the product of 5+6 and 7+8 are mixed, annealed, and extended for 10 cycles. Half of the two reactions are then mixed, and 5 cycles of annealing and extension carried out before flanking primers are added to amplify the full length product. The full-length product is gel-purified and cloned into pCR-blunt (Invitrogen) and individual clones are screened by sequencing.

Example 23 The Plasmid Construct and the Degree to which it Induces Immunogenicity

The degree to which a plasmid construct, for example a plasmid constructed in accordance with the previous Example, is able to induce immunogenicity is confirmed in vitro by determining epitope presentation by APC following transduction or transfection of the APC with an epitope-expressing nucleic acid construct. Such a study determines “antigenicity” and allows the use of human APC. The assay determines the ability of the epitope to be presented by the APC in a context that is recognized by a T cell by quantifying the density of epitope-HLA class I complexes on the cell surface. Quantitation can be performed by directly measuring the amount of peptide eluted from the APC (see, e.g., Sijts et al., J. Immunol. 156:683–692, 1996; Demotz et al., Nature 342:682–684, 1989); or the number of peptide-HLA class I complexes can be estimated by measuring the amount of lysis or lymphokine release induced by diseased or transfected target cells, and then determining the concentration of peptide necessary to obtain equivalent levels of lysis or lymphokine release (see, e.g., Kageyama et al., J. Immunol. 154:567–576, 1995).

Alternatively, immunogenicity is confirmed through in vivo injections into mice and subsequent in vitro assessment of CTL and HTL activity, which are analyzed using cytotoxicity and proliferation assays, respectively, as detailed e.g., in Alexander et al., Immunity 1:751–761, 1994.

For example, to confirm the capacity of a DNA minigene construct containing at least one HLA-A2 supermotif peptide to induce CTLs in vivo, HLA-A2.1l/K^(b) transgenic mice, for example, are immunized intramuscularly with 100 μg of naked cDNA. As a means of comparing the level of CTLs induced by cDNA immunization, a control group of animals is also immunized with an actual peptide composition that comprises multiple epitopes synthesized as a single polypeptide as they would be encoded by the minigene.

Splenocytes from immunized animals are stimulated twice with each of the respective compositions (peptide epitopes encoded in the minigene or the polyepitopic peptide), then assayed for peptide-specific cytotoxic activity in a ⁵¹Cr release assay. The results indicate the magnitude of the CTL response directed against the A2-restricted epitope, thus indicating the in vivo immunogenicity of the minigene vaccine and polyepitopic vaccine.

It is, therefore, found that the minigene elicits immune responses directed toward the HLA-A2 supermotif peptide epitopes as does the polyepitopic peptide vaccine. A similar analysis is also performed using other HLA-A3 and HLA-B7 transgenic mouse models to assess CTL induction by HLA-A3 and HLA-B7 motif or supermotif epitopes, whereby it is also found that the minigene elicits appropriate immune responses directed toward the provided epitopes.

To confirm the capacity of a class II epitope-encoding minigene to induce HTLs in vivo, DR transgenic mice, or for those epitopes that cross react with the appropriate mouse MHC molecule, I-A^(b)-restricted mice, for example, are immunized intramuscularly with 100 μg of plasmid DNA. As a means of comparing the level of HTLs induced by DNA immunization, a group of control animals is also immunized with an actual peptide composition emulsified in complete Freund's adjuvant. CD4+ T cells, i.e. HTLs, are purified from splenocytes of immunized animals and stimulated with each of the respective compositions (peptides encoded in the minigene). The HTL response is measured using a ³H-thymidine incorporation proliferation assay, (see, e.g., Alexander et al. Immunity 1:751–761, 1994). The results indicate the magnitude of the HTL response, thus demonstrating the in vivo immunogenicity of the minigene.

DNA minigenes, constructed as described in the previous Example, can also be confirmed as a vaccine in combination with a boosting agent using a prime boost protocol. The boosting agent can consist of recombinant protein (e.g., BarneU et al., Aids Res. and Human Retroviruses 14, Supplement 3:S299–S309, 1998) or recombinant vaccinia, for example, expressing a minigene or DNA encoding the complete protein of interest (see, e.g., Hanke et al., Vaccine 16:439–445, 1998; Sedegah et al., Proc. Natl. Acad. Sci USA 95:7648–53,1998; Hanke and McMichael, Immunol. Letters 66:177–181, 1999; and Robinson et al., Nature Med. 5:526–34, 1999).

For example, the efficacy of the DNA minigene used in a prime boost protocol is initially evaluated in transgenic mice. In this example, A2.1/K^(b) transgenic mice are immunized IM with 100 μg of a DNA minigene encoding the immunogenic peptides including at least one HLA-A2 supermotif-bearing peptide. After an incubation period (ranging from 3–9 weeks), the mice are boosted IP with 10⁷ pfu/mouse of a recombinant vaccinia virus expressing the same sequence encoded by the DNA minigene. Control mice are immunized with 100 μg of DNA or recombinant vaccinia without the minigene sequence, or with DNA encoding the minigene, but without the vaccinia boost. After an additional incubation period of two weeks, splenocytes from the mice are immediately assayed for peptide-specific activity in an ELISPOT assay. Additionally, splenocytes are stimulated in vitro with the A2-restricted peptide epitopes encoded in the minigene and recombinant vaccinia, then assayed for peptide-specific activity in an alpha, beta and/or gamma IFN ELISA.

It is found that the minigene utilized in a prime-boost protocol elicits greater immune responses toward the HLA-A2 supermotif peptides than with DNA alone. Such an analysis can also be performed using HLA-A11 or HLA-B7 transgenic mouse models to assess CTL induction by HLA-A3 or HLA-B7 motif or supermotif epitopes. The use of prime boost protocols in humans is described below in the Example entitled “Induction of CTL Responses Using a Prime Boost Protocol.”

Example 24 Peptide Compositions for Prophylactic Uses

Vaccine compositions of the present invention can be used to prevent 161P2F10B expression in persons who are at risk for tumors that bear this antigen. For example, a polyepitopic peptide epitope composition (or a nucleic acid comprising the same) containing multiple CTL and HTL epitopes such as those selected in the above Examples, which are also selected to target greater than 80% of the population, is administered to individuals at risk for a 161P2F10B-associated tumor.

For example, a peptide-based composition is provided as a single polypeptide that encompasses multiple epitopes. The vaccine is typically administered in a physiological solution that comprises an adjuvant, such as Incomplete Freunds Adjuvant. The dose of peptide for the initial immunization is from about 1 to about 50,000 μg, generally 100–5,000 μg, for a 70 kg patient. The initial administration of vaccine is followed by booster dosages at 4 weeks followed by evaluation of the magnitude of the immune response in the patient, by techniques that determine the presence of epitope-specific CTL populations in a PBMC sample. Additional booster doses are administered as required. The composition is found to be both safe and efficacious as a prophylaxis against 161P2F10B-associated disease.

Alternatively, a composition typically comprising transfecting agents is used for the administration of a nucleic acid-based vaccine in accordance with methodologies known in the art and disclosed herein.

Example 25 Polyepitopic Vaccine Compositions Derived from Native 161P2F10B Sequences

A native 161P2F10B polyprotein sequence is analyzed, preferably using computer algorithms defined for each class I and/or class II supermotif or motif, to identify “relatively short” regions of the polyprotein that comprise multiple epitopes. The “relatively short” regions are preferably less in length than an entire native antigen. This relatively short sequence that contains multiple distinct or overlapping, “nested” epitopes can be used to generate a minigene construct. The construct is engineered to express the peptide, which corresponds to the native protein sequence. The “relatively short” peptide is generally less than 250 amino acids in length, often less than 100 amino acids in length, preferably less than 75 amino acids in length, and more preferably less than 50 amino acids in length. The protein sequence of the vaccine composition is selected because it has maximal number of epitopes contained within the sequence, i.e., it has a high concentration of epitopes. As noted herein, epitope motifs may be nested or overlapping (ie., frame shifted relative to one another). For example, with overlapping epitopes, two 9-mer epitopes and one 10-mer epitope can be present in a 10 amino acid peptide. Such a vaccine composition is administered for therapeutic or prophylactic purposes.

The vaccine composition will include, for example, multiple CTL epitopes from 161P2F10B antigen and at least one HTL epitope. This polyepitopic native sequence is administered either as a peptide or as a nucleic acid sequence which encodes the peptide. Alternatively, an analog can be made of this native sequence, whereby one or more of the epitopes comprise substitutions that alter the cross-reactivity and/or binding affinity properties of the polyepitopic peptide.

The embodiment of this example provides for the possibility that an as yet undiscovered aspect of immune system processing will apply to the native nested sequence and thereby facilitate the production of therapeutic or prophylactic immune response-inducing vaccine compositions. Additionally, such an embodiment provides for the possibility of motif-bearing epitopes for an HLA makeup(s) that is presently unknown. Furthermore, this embodiment (excluding an analoged embodiment) directs the immune response to multiple peptide sequences that are actually present in native 161P2F10B, thus avoiding the need to evaluate any junctional epitopes. Lastly, the embodiment provides an economy of scale when producing peptide or nucleic acid vaccine compositions.

Related to this embodiment, computer programs are available in the art which can be used to identify in a target sequence, the greatest number of epitopes per sequence length.

Example 26 Polyepitopic Vaccine Compositions from Multiple Antigens

The 161P2F10B peptide epitopes of the present invention are used in conjunction with epitopes from other target tumor-associated antigens, to create a vaccine composition that is useful for the prevention or treatment of cancer that expresses 161P2F10B and such other antigens. For example, a vaccine composition can be provided as a single polypeptide that incorporates multiple epitopes from 161P2F10B as well as tumor-associated antigens that are often expressed with a target cancer associated with 161P2F10B expression, or can be administered as a composition comprising a cocktail of one or more discrete epitopes. Alternatively, the vaccine can be administered as a minigene construct or as dendritic cells which have been loaded with the peptide epitopes in vitro.

Example 27 Use of Peptides to Evaluate an Immune Response

Peptides of the invention may be used to analyze an immune response for the presence of specific antibodies, CTL or HTL directed to 161P2F10B. Such an analysis can be performed in a manner described by Ogg et al., Science 279:2103–2106, 1998. In this Example, peptides in accordance with the invention are used as a reagent for diagnostic or prognostic purposes, not as an immunogen.

In this example highly sensitive human leukocyte antigen tetrameric complexes (“tetramers”) are used for a cross-sectional analysis of, for example, 161P2F10B HLA-A*0201-specific CTL frequencies from HLA A*0201-positive individuals at different stages of disease or following immunization comprising a 161P2F10B peptide containing an A*0201 motif. Tetrameric complexes are synthesized as described (Musey et al., N. Engl. J. Med. 337:1267, 1997). Briefly, purified HLA heavy chain (A*0201 in this example) and β2-microglobulin are synthesized by means of a prokaryotic expression system. The heavy chain is modified by deletion of the transmembrane-cytosolic tail and COOH-terminal addition of a sequence containing a BirA enzymatic biotinylation site. The heavy chain, β2-microglobulin, and peptide are refolded by dilution. The 45-kD refolded product is isolated by fast protein liquid chromatography and then biotinylated by BirA in the presence of biotin (Sigma, St. Louis, Mo.), adenosine 5′ triphosphate and magnesium. Streptavidin-phycoerythrin conjugate is added in a 1:4 molar ratio, and the tetrameric product is concentrated to 1 mg/ml. The resulting product is referred to as tetramer-phycoerythrin.

For the analysis of patient blood samples, approximately one million PBMCs are centrifuged at 300 g for 5 minutes and resuspended in 50 μl of cold phosphate-buffered saline. Tri-color analysis is performed with the tetramer-phycoerythrin, along with anti-CD8-Tricolor, and anti-CD38. The PBMCs are incubated with tetramer and antibodies on ice for 30 to 60 min and then washed twice before formaldehyde fixation. Gates are applied to contain >99.98% of control samples. Controls for the tetramers include both A*0201-negative individuals and A*0201-positive non-diseased donors. The percentage of cells stained with the tetramer is then determined by flow cytometry. The results indicate the number of cells in the PBMC sample that contain epitope-restricted CTLs, thereby readily indicating the extent of immune response to the 161P2F10B epitope, and thus the status of exposure to 161P2F10B, or exposure to a vaccine that elicits a protective or therapeutic response.

Example 28 Use of Peptide Epitopes to Evaluate Recall Responses

The peptide epitopes of the invention are used as reagents to evaluate T cell responses, such as acute or recall responses, in patients. Such an analysis may be performed on patients who have recovered from 161P2F10B-associated disease or who have been vaccinated with a 161P2F10B vaccine.

For example, the class I restricted CTL response of persons who have been vaccinated may be analyzed. The vaccine may be any 161P2F10B vaccine. PBMC are collected from vaccinated individuals and HLA typed. Appropriate peptide epitopes of the invention that, optimally, bear supermotifs to provide cross-reactivity with multiple HLA supertype family members, are then used for analysis of samples derived from individuals who bear that HLA type.

PBMC from vaccinated individuals are separated on Ficoll-Histopaque density gradients (Sigma Chemical Co., St. Louis, Mo.), washed three times in HBSS (GIBCO Laboratories), resuspended in RPMI-1640 (GIBCO Laboratories) supplemented with L-glutamine (2 mM), penicillin (50 U/ml), streptomycin (50 μg/ml), and Hepes (10 mM) containing 10% heat-inactivated human AB serum (complete RPMI) and plated using microculture formats. A synthetic peptide comprising an epitope of the invention is added at 10 μg/ml to each well and HBV core 128–140 epitope is added at 1 μg/ml to each well as a source of T cell help during the first week of stimulation.

In the microculture format, 4×10⁵ PBMC are stimulated with peptide in 8 replicate cultures in 96-well round bottom plate in 100 μl/well of complete RPMI. On days 3 and 10, 100 μl of complete RPMI and 20 U/ml final concentration of rIL-2 are added to each well. On day 7 the cultures are transferred into a 96-well flat-bottom plate and restimulated with peptide, rIL-2 and 10⁵ irradiated (3,000 rad) autologous feeder cells. The cultures are tested for cytotoxic activity on day 14. A positive CTL response requires two or more of the eight replicate cultures to display greater than 10% specific ⁵¹Cr release, based on comparison with non-diseased control subjects as previously described (Rehermann, et al., Nature Med. 2:1104,1108, 1996; Rehermann et al., J. Clin. Invest. 97:1655–1665, 1996; and Rehermann et al. J. Clin. Invest. 98:1432–1440, 1996).

Target cell lines are autologous and allogeneic EBV-transformed B-LCL that are either purchased from the American Society for Histocompatibility and Immunogenetics (ASHI, Boston, Mass.) or established from the pool of patients as described (Guilhot, et al. J. Virol. 66:2670–2678, 1992).

Cytotoxicity assays are performed in the following manner. Target cells consist of either allogeneic HLA-matched or autologous EBV-transformed B lymphoblastoid cell line that are incubated overnight with the synthetic peptide epitope of the invention at 10 μM, and labeled with 100 μCi of ⁵¹Cr (Amersham Corp., Arlington Heights, Ill.) for 1 hour after which they are washed four times with HBSS.

Cytolytic activity is determined in a standard 4-h, split well ⁵¹Cr release assay using U-bottomed 96 well plates containing 3,000 targets/well. Stimulated PBMC are tested at effector/target (E/T) ratios of 20–50:1 on day 14. Percent cytotoxicity is determined from the formula: 100×[(experimental release-spontaneous release)/maximum release-spontaneous release)]. Maximum release is determined by lysis of targets by detergent (2% Triton X-100; Sigma Chemical Co., St. Louis, Mo.). Spontaneous release is <25% of maximum release for all experiments.

The results of such an analysis indicate the extent to which HLA-restricted CTL populations have been stimulated by previous exposure to 161P2F10B or a 161P2F10B vaccine.

Similarly, Class II restricted HTL responses may also be analyzed. Purified PBMC are cultured in a 96-well flat bottom plate at a density of 1.5×10⁵ cells/well and are stimulated with 10 μg/ml synthetic peptide of the invention, whole 161P2F10B antigen, or PHA. Cells are routinely plated in replicates of 4–6 wells for each condition. After seven days of culture, the medium is removed and replaced with fresh medium containing 10 U/ml IL-2. Two days later, 1 μCi ³H-thymidine is added to each well and incubation is continued for an additional 18 hours. Cellular DNA is then harvested on glass fiber mats and analyzed for ³H-thymidine incorporation. Antigen-specific T cell proliferation is calculated as the ratio of ³H-thymidine incorporation in the presence of antigen divided by the ³H-thymidine incorporation in the absence of antigen.

Example 29 Induction of Specific CTL Response in Humans

A human clinical trial for an immunogenic composition comprising CTL and HTL epitopes of the invention is set up as an IND Phase I, dose escalation study and carried out as a randomized, double-blind, placebo-controlled trial. Such a trial is designed, for example, as follows:

A total of about 27 individuals are enrolled and divided into 3 groups:

Group I: 3 subjects are injected with placebo and 6 subjects are injected with 5 μg of peptide composition;

Group II: 3 subjects are injected with placebo and 6 subjects are injected with 50 μg peptide composition;

Group III: 3 subjects are injected with placebo and 6 subjects are injected with 500 μg of peptide composition.

After 4 weeks following the first injection, all subjects receive a booster inoculation at the same dosage.

The endpoints measured in this study relate to the safety and tolerability of the peptide composition as well as its immunogenicity. Cellular immune responses to the peptide composition are an index of the intrinsic activity of this the peptide composition, and can therefore be viewed as a measure of biological efficacy. The following summarize the clinical and laboratory data that relate to safety and efficacy endpoints.

Safety: The incidence of adverse events is monitored in the placebo and drug treatment group and assessed in terms of degree and reversibility.

Evaluation of Vaccine Efficacy: For evaluation of vaccine efficacy, subjects are bled before and after injection. Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.

The vaccine is found to be both safe and efficacious.

Example 30 Phase II Trials in Patients Expressing 161P2F10B

Phase II trials are performed to study the effect of administering the CTL-HTL peptide compositions to patients having cancer that expresses 161P2F10B. The main objectives of the trial are to determine an effective dose and regimen for inducing CTLs in cancer patients that express 161P2F10B, to establish the safety of inducing a CTL and HTL response in these patients, and to see to what extent activation of CTLs improves the clinical picture of these patients, as manifested, e.g., by the reduction and/or shrinking of lesions. Such a study is designed, for example, as follows:

The studies are performed in multiple centers. The trial design is an open-label, uncontrolled, dose escalation protocol wherein the peptide composition is administered as a single dose followed six weeks later by a single booster shot of the same dose. The dosages are 50, 500 and 5,000 micrograms per injection. Drug-associated adverse effects (severity and reversibility) are recorded.

There are three patient groupings. The first group is injected with 50 micrograms of the peptide composition and the second and third groups with 500 and 5,000 micrograms of peptide composition, respectively. The patients within each group range in age from 21–65 and represent diverse ethnic backgrounds. All of them have a tumor that expresses 161P2F10B.

Clinical manifestations or antigen-specific T-cell responses are monitored to assess the effects of administering the peptide compositions. The vaccine composition is found to be both safe and efficacious in the treatment of 161P2F10B-associated disease.

Example 31 Induction of CTL Responses Using a Prime Boost Protocol

A prime boost protocol similar in its underlying principle to that used to confirm the efficacy of a DNA vaccine in transgenic mice, such as described above in the Example entitled “The Plasmid Construct and the Degree to Which It Induces Immunogenicity,” can also be used for the administration of the vaccine to humans. Such a vaccine regimen can include an initial administration of, for example, naked DNA followed by a boost using recombinant virus encoding the vaccine, or recombinant protein/polypeptide or a peptide mixture administered in an adjuvant.

For example, the initial immunization may be performed using an expression vector, such as that constructed in the Example entitled “Construction of “Minigene” Multi-Epitope DNA Plasmids” in the form of naked nucleic acid administered IM (or SC or ID) in the amounts of 0.5–5 mg at multiple sites. The nucleic acid (0.1 to 1000 μg) can also be administered using a gene gun. Following an incubation period of 3–4 weeks, a booster dose is then administered. The booster can be recombinant fowlpox virus administered at a dose of 5–10⁷ to 5×10⁹ pfu. An alternative recombinant virus, such as an MVA, canarypox, adenovirus, or adeno-associated virus, can also be used for the booster, or the polyepitopic protein or a mixture of the peptides can be administered. For evaluation of vaccine efficacy, patient blood samples are obtained before immunization as well as at intervals following administration of the initial vaccine and booster doses of the vaccine. Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.

Analysis of the results indicates that a magnitude of response sufficient to achieve a therapeutic or protective immunity against 161P2F10B is generated.

Example 32 Administration of Vaccine Compositions Using Dendritic Cells (DC)

Vaccines comprising peptide epitopes of the invention can be administered using APCs, or “professional” APCs such as DC. In this example, peptide-pulsed DC are administered to a patient to stimulate a CTL response in vivo. In this method, dendritic cells are isolated, expanded, and pulsed with a vaccine comprising peptide CTL and HTL epitopes of the invention. The dendritic cells are infused back into the patient to elicit CTL and HTL responses in vivo. The induced CTL and HTL then destroy or facilitate destruction, respectively, of the target cells that bear the 161P2F10B protein from which the epitopes in the vaccine are derived.

For example, a cocktail of epitope-comprising peptides is administered ex vivo to PBMC, or isolated DC therefrom. A pharmaceutical to facilitate harvesting of DC can be used, such as Progenipoietin™ (Monsanto, St. Louis, Mo.) or GM-CSF/IL-4. After pulsing the DC with peptides, and prior to reinfusion into patients, the DC are washed to remove unbound peptides.

As appreciated clinically, and readily determined by one of skill based on clinical outcomes, the number of DC reinfused into the patient can vary (see, e.g., Nature Med. 4:328, 1998; Nature Med. 2:52, 1996 and Prostate 32:272, 1997). Although 2–50×10⁶ DC per patient are typically administered, larger number of DC, such as 10⁷ or 10⁸ can also be provided. Such cell populations typically contain between 50–90% DC.

In some embodiments, peptide-loaded PBMC are injected into patients without purification of the DC. For example, PBMC generated after treatment with an agent such as Progenipoietin™ are injected into patients without purification of the DC. The total number of PBMC that are administered often ranges from 10⁸ to 10¹⁰. Generally, the cell doses injected into patients is based on the percentage of DC in the blood of each patient, as determined, for example, by immunofluorescence analysis with specific anti-DC antibodies. Thus, for example, if Progenipoietin™ mobilizes 2% DC in the peripheral blood of a given patient, and that patient is to receive 5×10⁶ DC, then the patient will be injected with a total of 2.5×10⁸ peptide-loaded PBMC. The percent DC mobilized by an agent such as Progenipoietin™ is typically estimated to be between 2–10%, but can vary as appreciated by one of skill in the art.

Ex Vivo Activation of CTL/HTL Responses

Alternatively, ex vivo CTL or HTL responses to 161P2F10B antigens can be induced by incubating, in tissue culture, the patient's, or genetically compatible, CTL or HTL precursor cells together with a source of APC, such as DC, and immunogenic peptides. After an appropriate incubation time (typically about 7–28 days), in which the precursor cells are activated and expanded into effector cells, the cells are infused into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cells, i.e., tumor cells.

Example 33 An Alternative Method of Identifying and Confirming Motif-Bearing Peptides

Another method of identifying and confirming motif-bearing peptides is to elute them from cells bearing defined MHC molecules. For example, EBV transformed B cell lines used for tissue typing have been extensively characterized to determine which HLA molecules they express. In certain cases these cells express only a single type of HLA molecule. These cells can be transfected with nucleic acids that express the antigen of interest, e.g. 161P2F10B. Peptides produced by endogenous antigen processing of peptides produced as a result of transfection will then bind to HLA molecules within the cell and be transported and displayed on the cell's surface. Peptides are then eluted from the HLA molecules by exposure to mild acid conditions and their amino acid sequence determined, e.g., by mass spectral analysis (e.g., Kubo et al., J. Immunol. 152:3913, 1994). Because the majority of peptides that bind a particular HLA molecule are motif-bearing, this is an alternative modality for obtaining the motif-bearing peptides correlated with the particular HLA molecule expressed on the cell.

Alternatively, cell lines that do not express endogenous HLA molecules can be transfected with an expression construct encoding a single HLA allele. These cells can then be used as described, i.e., they can then be transfected with nucleic acids that encode 161P2F10B to isolate peptides corresponding to 161P2F10B that have been presented on the cell surface. Peptides obtained from such an analysis will bear motif(s) that correspond to binding to the single HLA allele that is expressed in the cell.

As appreciated by one in the art, one can perform a similar analysis on a cell bearing more than one HLA allele and subsequently determine peptides specific for each HLA allele expressed. Moreover, one of skill would also recognize that means other than transfection, such as loading with a protein antigen, can be used to provide a source of antigen to the cell.

Example 34 Complementary Polynucleotides

Sequences complementary to the 161P2F10B-encoding sequences, or any parts thereof, are used to detect, decrease, or inhibit expression of naturally occurring 161P2F10B. Although use of oligonucleotides comprising from about 15 to 30 base pairs is described, essentially the same procedure is used with smaller or with larger sequence fragments. Appropriate oligonucleotides are designed using, e.g., OLIGO 4.06 software (National Biosciences) and the coding sequence of 161P2F10B. To inhibit transcription, a complementary oligonucleotide is designed from the most unique 5′ sequence and used to prevent promoter binding to the coding sequence. To inhibit translation, a complementary oligonucleotide is designed to prevent ribosomal binding to a 161P2F10B-encoding transcript.

Example 35 Purification of Naturally-occurring or Recombinant 161P2F10B Using 161P2F10B-Specific Antibodies

Naturally occurring or recombinant 161P2F10B is substantially purified by immunoaffinity chromatography using antibodies specific for 161P2F10B. An immunoaffinity column is constructed by covalently coupling anti-161P2F10B antibody to an activated chromatographic resin, such as CNBr-activated SEPHAROSE (Amersham Pharmacia Biotech). After the coupling, the resin is blocked and washed according to the manufacturers instructions.

Media containing 161P2F10B are passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of 161P2F10B (e.g., high ionic strength buffers in the presence of detergent). The column is eluted under conditions that disrupt antibody/161P2F10B binding (e.g., a buffer of pH 2 to pH 3, or a high concentration of a chaotrope, such as urea or thiocyanate ion), and GCRP is collected.

Example 36 Identification of Molecules which Interact with 161P2F10B

161P2F10B, or biologically active fragments thereof, are labeled with 121 1 Bolton-Hunter reagent. (See, e.g., Bolton et al. (1973) Biochem. J. 133:529.) Candidate molecules previously arrayed in the wells of a multi-well plate are incubated with the labeled 161P2F10B, washed, and any wells with labeled 161P2F10B complex are assayed. Data obtained using different concentrations of 161P2F10B are used to calculate values for the number, affinity, and association of 161P2F10B with the candidate molecules.

Example 37 In Vivo Assay for 161P2F10B Tumor Growth Promotion

The effect of the 161P2F10B protein on tumor cell growth is evaluated in vivo by gene overexpression in tumor-bearing mice. For example, SCID mice are injected subcutaneously on each flank with 1×10⁶ of either PC3, TSUPR1, or DU145cells containing tkNeo empty vector or 161P2F10B. At least two strategies may be used: (1) Constitutive 161P2F10B expression under regulation of a promoter such as a constitutive promoter obtained from the genomes of viruses such as polyoma virus, fowlpox virus (UK 2,211,504 published 5 Jul. 1989), adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), or from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, provided such promoters are compatible with the host cell systems, and (2) regulated expression under control of an inducible vector system, such as ecdysone, tet, etc., provided such promoters are compatible with the host cell systems. Tumor volume is then monitored at the appearance of palpable tumors and followed over time and determines that 161P2F10B-expressing cells grow at a faster rate and/or tumors produced by 161P2F10B-expressing cells demonstrate characteristics of altered aggressiveness (e.g. enhanced metastasis, vascularization, reduced responsiveness to chemotherapeutic drugs).

Additionally, mice can be implanted with 1×10⁵ of the same cells orthotopically to determine that 161P2F10B has an effect on local growth in the prostate and/or on the ability of the cells to metastasize, e.g., to lungs, lymph nodes, and bone marrow.

The assay is also useful to determine the 161P2F10B-inhibitory effect of candidate therapeutic compositions, such as for example, small molecule drugs, 161P2F10B intrabodies, 161P2F10B antisense molecules and ribozymes.

Example 38 161P2F10B Monoclonal Antibody-mediated Inhibition of Prostate Tumors In Vivo

The significant expression of 161P2F10B, in cancer tissues, together with its restricted expression in normal tissues along with its cell surface expression makes 161P2F10B an excellent target for antibody therapy. Similarly, 161P2F10B is a target for T cell-based immunotherapy. Thus, the therapeutic efficacy of anti-161P2F10B mAbs is evaluated, e.g., in human prostate cancer xenograft mouse models using androgen-independent LAPC-4 and LAPC-9 xenografts (Craft, N., et al., Cancer Res, 1999. 59(19): p. 5030–6), kidney cancer xenografts (AGS-K3, AGS-K6), kidney cancer metastases to lymph node (AGS-K6 met) xenografts, and kidney cancer cell lines transfected with 161P2F10B, such as 769P-161P2F10B, A498-161P2F10B.

Antibody efficacy on tumor growth and metastasis formation is studied, e.g., in mouse orthotopic prostate cancer xenograft models and mouse kidney xenograft models. The antibodies can be unconjugated, as discussed in this Example, or can be conjugated to a therapeutic modality, as appreciated.in the art. Anti-161P2F10B mAbs inhibit formation of both the androgen-dependent LAPC-9 and androgen-independent PC3-161P2F10B tumor xenografls. Anti-161P2F10B mAbs also retard the growth of established orthotopic tumors and prolonged survival of tumor-bearing mice. These results indicate the utility of anti-161P2F10B mAbs in the treatment of local and advanced stages of prostate cancer. (See, e.g., Saffran, D., et al., PNAS 10:1073–1078. Similarly, anti-161P2F10B mAbs can inhibit formation of AGS-K3 and AGS-K6 tumors in SCID mice, and prevent or retard the growth A498-161P2F10B tumor xenografts. These results indicate the use of anti-161P2F10B mAbs in the treatment of prostate and/or kidney cancer.

Administration of the anti-161P2F10B mAbs leads to retardation of established orthotopic tumor growth and inhibition of metastasis to distant sites, resulting in a significant prolongation in the survival of tumor-bearing mice. These studies indicate that 161P2F10B is an attractive target for immunotherapy and demonstrate the therapeutic use of anti-161P2F10B mAbs for the treatment of local and metastatic prostate cancer. This example demonstrates that unconjugated 161P2F10B monoclonal antibodies are effective to inhibit the growth of human prostate tumor xenografts and human kidney xenografts grown in SCID mice.

Tumor Inhibition Using Multiple Unconjugated 161P2F10B mAbs

Materials and Methods

161P2F10B Monoclonal Antibodies:

Monoclonal antibodies are raised against 161P2F10B as described in the Example entitled “Generation of 161P2F10B Monoclonal Antibodies (mAbs)” or are obtained commercially, e.g., 97A6 (Coulter Immunotech). The antibodies are characterized by ELISA, Western blot, FACS, and immunoprecipitation for their capacity to bind 161P2F10B. Epitope mapping data for the anti-161P2F10B mAbs, as determined by ELISA and Western analysis, recognize epitopes on the 161P2F10B protein. The 97A6 antibody binds to amino acids 393–405 of the 161P2F10B protein shown in FIG. 2. Immunohistochemical analysis of cancer tissues and cells is performed with these antibodies.

The monoclonal antibodies are purified from ascites or hybridoma tissue culture supernatants by Protein-G Sepharose chromatography, dialyzed against PBS, filter sterilized, and stored at −20° C. Protein determinations are performed by a Bradford assay (Bio-Rad, Hercules, Calif.). A therapeutic monoclonal antibody or a cocktail comprising a mixture of individual monoclonal antibodies is prepared and used for the treatment of mice receiving subcutaneous or orthotopic injections of LAPC-9 prostate tumor xenografts.

Cancer Xenografts and Cell Lines

The LAPC-9 xenograft, which expresses a wild-type androgen receptor and produces prostate-specific antigen (PSA), is passaged in 6- to 8-week-old male ICR-severe combined immunodeficient (SCID) mice (Taconic Farms) by s.c. trocar implant (Craft, N., et al., supra). The AGS-K3 and AGS-K6 kidney xenografts are also passaged by subcutaneous implants in 6- to 8-week old SCID mice. Single-cell suspensions of tumor cells are prepared as described in Craft, et al. The prostate carcinoma cell line PC3 (American Type Culture Collection) is maintained in RPMI supplemented with L-glutamine and 10% FBS, and the kidney carcinoma line A498 (American Type Culture Collection) is maintained in DMEM supplemented with L-glutamine and 10% FBS.

PC3-161P2F10B and A498-161P2F10B cell populations are generated by retroviral gene transfer as described in Hubert, R. S., et al., STEAP: A Prostate-specific Cell-surface Antigen Highly Expressed in Human Prostate Tumors, Proc Natl Acad Sci USA, 1999. 96(25): p. 14523–8. Anti-161P2F10B staining is detected by using an FITC-conjugated goatanti-mouse antibody (Southern Biotechnology Associates) followed by analysis on a Coulter Epics-XL f low cytometer.

Xenograft Mouse Models.

Subcutaneous (s.c.) tumors are generated by injection of 1×10⁶ LAPC-9, AGS-K3, AGS-K6, PC3, PC3-161P2F10B, A498 or A498-161P2F10B cells mixed at a 1:1 dilution with Matrigel (Collaborative Research) in the right flank of male SCID mice. To test antibody efficacy on tumor formation, i.p. antibody injections are started on the same day as tumor-cell injections. As a control, mice are injected with either purified mouse IgG (ICN) or PBS; or a purified monoclonal antibody that recognizes an irrelevant antigen not expressed in human cells. In preliminary studies, no difference is found between mouse IgG or PBS on tumor growth. Tumor sizes are determined by vernier caliper measurements, and the tumor volume is calculated as length×width×height. Mice with s.c. tumors greater than 1.5 cm in diameter are sacrificed. PSA levels are determined by using a PSA ELISA kit (Anogen, Mississauga, Ontario). Circulating levels of anti-161P2F10B mAbs are determined by a capture ELISA kit (Bethyl Laboratories, Montgomery, Tex.). (See, e.g., (Saffran, D., et al., PNAS 10:1073–1078.

Orthotopic prostate injections are performed under anesthesia by using ketamine/xylazine. For prostate orthotopic studies, an incision is made through the abdominal muscles to expose the bladder and seminal vesicles, which then are delivered through the incision to expose the dorsal prostate. LAPC-9 cells (5×10⁵) mixed with Matrigel are injected into each dorsal lobe in a 10-μl volume. To monitor tumor growth, mice are bled on a weekly basis for determination of PSA levels. For kidney orthopotic models, an incision is made through the abdominal muscles to expose the kidney. AGS-K3 or AGS-K6 cells mixed with Matrigel are injected under the kidney capsule. The mice are segregated into groups for the appropriate treatments, with anti-161P2F10B or control mAbs being injected i.p.

Anti-161P2F10B mAbs Inhibit Growth of 161P2F10B-Expressing Xenograft-Cancer Tumors

The effect of anti-161P2F10B mAbs on tumor formation is tested by using LAPC-9 and/or AGS-K3 orthotopic models. As compared with the s.c. tumor model, the orthotopic model, which requires injection of tumor cells directly in the mouse prostate or kidney, respectively, results in a local tumor growth, development of metastasis in distal sites, deterioration of mouse health, and subsequent death (Saffran, D., et al., PNAS supra; Fu, X., et al., Int J Cancer, 1992. 52(6): p. 987–90; Kubota, T., J Cell Biochem, 1994. 56(1): p. 4–8). The features make the orthotopic model more representative of human disease progression and allowed for tracking of the therapeutic effect of mAbs on clinically relevant end points.

Accordingly, tumor cells are injected into the mouse prostate or kidney, and 2 days later, the mice are segregated into two groups and treated with either: a) 200–500 μg, of anti-161P2F10B Ab, or b) PBS three times per week for two to five weeks.

A major advantage of the orthotopic prostate-cancer model is the ability to study the development of metastases. Formation of metastasis in mice bearing established orthotopic tumors is studies by IHC analysis on lung sections using an antibody against a prostate-specific cell-surface protein STEAP expressed at high levels in LAPC-9 xenografts (Hubert, R. S., et al., Proc Natl Acad Sci USA, 1999. 96(25): p. 14523–8) or anti-G250 antibody for kidney cancer models.

Mice bearing established orthotopic LAPC-9 tumors are administered 1000 μg injections of either anti-161P2F10B mAb or PBS over a 4-week period. Mice in both groups are allowed to establish a high tumor burden (PSA levels greater than 300 ng/ml), to ensure a high frequency of metastasis formation in mouse lungs. Mice then are killed and their prostate/kidney and lungs are analyzed for the presence of tumor cells by IHC analysis.

These studies demonstrate a broad anti-tumor efficacy of anti-161P2F10B antibodies on initiation and progression of prostate and kidney cancer in xenograft mouse models. Anti-161P2F10B antibodies inhibit tumor formation of both androgen-dependent and androgen-independent prostate tumors as well as retarding the growth of already established tumors and prolong the survival of treated mice. Moreover, anti-161P2F10B mAbs demonstrate a dramatic inhibitory effect on the spread of local prostate tumor to distal sites, even in the presence of a large tumor burden. Similar therapeutic effects are seen in the kidney cancer model. Thus, anti-161P2F10B mAbs are efficacious on major clinically relevant end points (tumor growth), prolongation of survival, and health.

Example 39 Therapeutic and Diagnostic use of Anti-161P2F10B Antibodies in Humans

Anti-161P2F10B monoclonal antibodies are safely and effectively used for diagnostic, prophylactic, prognostic and/or therapeutic purposes in humans. Western blot and immunohistochemical analysis of cancer tissues and cancer xenografts with anti-161P2F10B mAb show strong extensive staining in carcinoma but significantly lower or undetectable levels in normal tissues. Detection of 161P2F10B in carcinoma and in metastatic disease demonstrates the usefulness of the mAb as a diagnostic and/or prognostic indicator. Anti-161P2F10B antibodies are therefore used in diagnostic applications such as immunohistochemistry of kidney biopsy specimens to detect cancer from suspect patients.

As determined by flow cytometry, anti-161P2F10B mAb specifically binds to carcinoma cells. Thus, anti-161P2F10B antibodies are used in diagnostic whole body imaging applications, such as radioimmunoscintigraphy and radioimmunotherapy, (see, e.g., Potamianos S., et. al. Anticancer Res 20(2A):925–948 (2000)) for the detection of localized and metastatic cancers that exhibit expression of 161P2F10B. Shedding or release of an extracellular domain of 161P2F10B into the extracellular milieu, such as that seen for alkaline phosphodiesterase B10 (Meerson, N. R., Hepatology 27:563–568 (1998)), allows diagnostic detection of 161P2F10B by anti-161P2F10B antibodies in serum and/or urine samples from suspect patients.

Anti-161P2F10B antibodies that specifically bind 161P2F10B are used in therapeutic applications for the treatment of cancers that express 161P2F10B. Anti-161P2F10B antibodies are used as an unconjugated modality and as conjugated form in which the antibodies are attached to one of various therapeutic or imaging modalities well known in the art, such as a prodrugs, enzymes or radioisotopes. In preclinical studies, unconjugated and conjugated anti-161P2F10B antibodies are tested for efficacy of tumor prevention and growth inhibition in the SCID mouse cancer xenograft models, e.g., kidney cancer models AGS-K3 and AGS-K6, (see, e.g., the Example entitled “161P2F10B Monoclonal Antibody-mediated Inhibition of Bladder and Lung Tumors In Vivo”). Either conjugated and unconjugated anti-61 P2F10B antibodies are used as a therapeutic modality in human clinical trials either alone or in combination with other treatments as described in following Examples.

Example 40 Human Clinical Trials for the Treatment and Diagnosis of Human Carcinomas through use of Human Anti-161P2F10B Antibodies In Vivo

Antibodies are used in accordance with the present invention which recognize an epitope on 161P2F10B, and are used in the treatment of certain tumors such as those listed in Table I. Based upon a number of factors, including 161P2F10B expression levels, tumors such as those listed in Table I are presently preferred indications. In connection with each of these indications, three clinical approaches are successfully pursued.

I.) Adjunctive therapy: In adjunctive therapy, patients are treated with anti-161P2F10B antibodies in combination with a chemotherapeutic or antineoplastic agent and/or radiation therapy. Primary cancer targets, such as those listed in Table I, are treated under standard protocols by the addition anti-161P2F10B antibodies to standard first and second line therapy. Protocol designs address effectiveness as assessed by reduction in tumor mass as well as the ability to reduce usual doses of standard chemotherapy. These dosage reductions allow additional and/or prolonged therapy by reducing dose-related toxicity of the chemotherapeutic agent. Anti-161P2F10B antibodies are utilized in several adjunctive clinical trials in combination with the chemotherapeutic or antineoplastic agents adriamycin (advanced prostrate carcinoma), cisplatin (advanced head and neck and lung carcinomas), taxol (breast cancer), and doxorubicin (preclinical).

II.) Monotherapy: In connection with the use of the anti-161P2F10B antibodies in monotherapy of tumors, the antibodies are administered to patients without a chemotherapeutic or antineoplastic agent. In one embodiment, monotherapy is conducted clinically in end stage cancer patients with extensive metastatic disease. Patients show some disease stabilization. Trials demonstrate an effect in refractory patients with cancerous tumors.

III.) Imaging Agent: Through binding a radionuclide (e.g., iodine or yttrium (I¹³¹, Y⁹⁰) to anti-161P2F10B antibodies, the radiolabeled antibodies are utilized as a diagnostic and/or imaging agent. In such a role, the labeled antibodies localize to both solid tumors, as well as, metastatic lesions of cells expressing 161P2F10B. In connection with the use of the anti-161P2F10B antibodies as imaging agents, the antibodies are used as an adjunct to surgical treatment of solid tumors, as both a pre-surgical screen as well as a post-operative follow-up to determine what tumor remains and/or returns. In one embodiment, a (¹¹¹In)-161P2F10B antibody is used as an imaging agent in a Phase I human clinical trial in patients having a carcinoma that expresses 161P2F10B (by analogy see, e.g., Divgi et al. J. Natl. Cancer Inst. 83:97–104 (1991)). Patients are followed with standard anterior and posterior gamma camera. The results indicate that primary lesions and metastatic lesions are identified.

Dose and Route of Administration

As appreciated by those of ordinary skill in the art, dosing considerations can be determined through comparison with the analogous products that are in the clinic. Thus, anti-161P2F10B antibodies can be administered with doses in the range of 5 to 400 mg/m², with the lower doses used, e.g., in connection with safety studies. The affinity of anti-161P2F10B antibodies relative to the affinity of a known antibody for its target is one parameter used by those of skill in the art for determining analogous dose regimens. Further, anti-161P2F10B antibodies that are fully human antibodies, as compared to the chimeric antibody, have slower clearance; accordingly, dosing in patients with such fully human anti-161P2F10B antibodies can be lower, perhaps in the range of 50 to 300 mg/m², and still remain efficacious. Dosing in mg/m², as opposed to the conventional measurement of dose in mg/kg, is a measurement based on surface area and is a convenient dosing measurement that is designed to include patients of all sizes from infants to adults.

Three distinct delivery approaches are useful for delivery of anti-161P2F10B antibodies. Conventional intravenous delivery is one standard delivery technique for many tumors. However, in connection with tumors in the peritoneal cavity, such as tumors of the ovaries, biliary duct, other ducts, and the like, intraperitoneal administration may prove favorable for obtaining high dose of antibody at the tumor and to also minimize antibody clearance. In a similar manner, certain solid tumors possess vasculature that is appropriate for regional perfusion. Regional perfusion allows for a high dose of antibody at the site of a tumor and minimizes short term clearance of the antibody.

Clinical Development Plan (CDP)

Overview: The CDP follows and develops treatments of anti-161P2F10B antibodies in connection with adjunctive therapy, monotherapy, and as an imaging agent. Trials initially demonstrate safety and thereafter confirm efficacy in repeat doses. Trails are open label comparing standard chemotherapy with standard therapy plus anti-161P2F10B antibodies. As will be appreciated, one criteria that can be utilized in connection with enrollment of patients is 161P2F10B expression levels in their tumors as determined by biopsy.

As with any protein or antibody infusion-based therapeutic, safety concerns are related primarily to (i) cytokine release syndrome, i.e., hypotension, fever, shaking, chills; (ii) the development of an immunogenic response to the material (i.e., development of human antibodies by the patient to the antibody therapeutic, or HAHA response); and, (iii) toxicity to normal cells that express 161P2F10B. Standard tests and follow-up are utilized to monitor each of these safety concerns. Anti-161P2F10B antibodies are found to be safe upon human administration.

Example 41 Human Clinical Trial Adjunctive Therapy with Human Anti-161P2F10B Antibody and Chemotherapeutic Agent

A phase I human clinical trial is initiated to assess the safety of six intravenous doses of a human anti-161P2F10B antibody in connection with the treatment of a solid tumor, e.g., a cancer of a tissue listed in Table I. In the study, the safety of single doses of anti-161P2F10B antibodies when utilized as an adjunctive therapy to an antineoplastic or chemotherapeutic agent as defined herein, such as, without limitation: cisplatin, topotecan, doxorubicin, adriamycin, taxol, or the like, is assessed. The trial design includes delivery of six single doses of an anti-161P2F10B antibody with dosage of antibody escalating from approximately about 25 mg/M ² to about 275 mg/m ² over the course of the treatment in accordance with the following schedule:

Day 0 Day 7 Day 14 Day 21 Day 28 Day 35 mAb Dose 25 75 125 175 225 275 mg/m² mg/m² mg/m² mg/m² mg/m² mg/m² Chemotherapy + + + + + + (standard dose)

Patients are closely followed for one-week following each administration of antibody and chemotherapy. In particular, patients are assessed for the safety concerns mentioned above: (i) cytokine release syndrome, i.e., hypotension, fever, shaking, chills; (ii) the development of an immunogenic response to the material (i.e., development of human antibodies by the patient to the human antibody therapeutic, or HAHA response); and, (iii) toxicity to normal cells that express 161P2F10B. Standard tests and follow-up are uilized to monitor each of these safety concerns. Patients are also assessed for clinical outcome, and particularly reduction in tumor mass as evidenced by MRI or other imaging.

The anti-161P2F10B antibodies are demonstrated to be safe and efficacious, Phase II trials confirm the efficacy and refine optimum dosing.

Example 42 Human Clinical Trial: Monotherapy with Human Anti-161P2F10B Antibody

Anti-161P2F10B antibodies are safe in connection with the above-discussed adjunctive trial, a Phase II human clinical trial confirms the efficacy and optimum dosing for monotherapy. Such trial is accomplished, and entails the same safety and outcome analyses, to the above-described adjunctive trial with the exception being that patients do not receive chemotherapy concurrently with the receipt of doses of anti-161P2F10B antibodies.

Example 43 Human Clinical Trial: Diagnostic Imaging with Anti-161P2F10B Antibody

Once again, as the adjunctive therapy discussed above is safe within the safety criteria discussed above, a human clinical trial is conducted concerning the use of anti-161P2F10B antibodies as a diagnostic imaging agent. The protocol is designed in a substantially similar manner to those described in the art, such as in Divgi et al. J. Natl. Cancer Inst. 83:97–104 (1991). The antibodies are found to be both safe and efficacious when used as a diagnostic modality.

Example 44 Homology Comparison of 161P2F10B to Known Sequences

The 161P2F10B gene is identical to a previously cloned and sequenced gene, namely ectonucleotide pyrophosphatase/phosphodiesterase 3 (gi 4826896) (Jin-Hua P et al, Genomics 1997, 45:412), also known as phosphodiesterase-I beta; gp130RB13-6; E-NPP3 (ENPP3), PDNP3 and CD203c. The 161P2F10B protein shows 100% identity to human ectonucleotide pyrophosphatase/phosphodiesterase 3 (gi 4826896), and 81% homology and 89% identity to rat alkaline phosphodiesterase (gi 1699034). The 161P2F10B protein consists of 875 amino acids, with calculated molecular weight of 100.09 kDa, and pI of 6.12. 161P2F10B is a cell surface protein as shown by immunostaining in basophils (Buhring H J et al, Blood 2001, 97:3303) and in epithelial tumor cells as shown in the example entitled “Expression of 161P2F10B protein in kidney cancer xenograft tissues”. Some localization to the golgi-endoplasmic fraction has also been observed (Geoffroy V et al, Arch Biochem Biophys. 2001, 387:154). Two isoforms of phosphodiesterase 3 have been identified, with one protein containing an additional 145 aa at its amino-tenninus (Choi Y H et al, Biochem J. 2001, 353:41). In addition, two variants of 161P2F10B have been identified. The first variant contains a point mutation at amino acid 122 of the 161P2F10B protein, changing a lysine to an arginine at that position. The second variant contains a single nucleotide polymorphisms, identified at position 383, resulting in a change in amino acid from threonine to proline at that position (FIG. 4A and 4B). In addition, we have recently identified another variant of 161P2F10B, namely 161P2F10B v.7. This variant differs from v.1 at its N-terminus as it lacks the first 34 aa found in v.1. The loss of the N-terminal 34 aa affects the localization of 161P2F10B v.7. PSort analysis reveled that, while 161P2F10B v.1 is primarily located at the plasma membrane, 161P2F10B v.7 primarily localizes to the cytoplasm (52%) with some localization to the nucleus (17%).

Motif analysis revealed the presence of several known motifs, including 2–3 somatostatin B domains located at the amino terminus of the 161P2F10B protein, a phosphodiesterase domain and an endonuclease domain at the C-terminus. 161P2F10B belongs to a family of closely related phosphodiesterases, consisting of PDNP1, -2, and -3 (Bollen M et al, Crit. Rev. Biochem Mol. Biol. 2000, 35: 393). All three members of this family are type 11 proteins, with a short N-terminus domain located intracellularly. They contain one transmembrane domain, a catalytic phosphodiesterase domain and a C-terminal nuclease domain.

Phosphodiesterase 3 expression has been detected in human neoplastic submandibular cells, glioma cells, and tansformed lymphocytes (Murata T et al, Anticancer Drugs 2001, 12:79; Andoh K et al, Biochim Biophys Acta 1999, 1446:213; Ekholm D et al, Biochem Pharmacol 1999, 58: 935).

Phosphodiesterase 3 plays an important role in several biological processes, including release of nucleotides, cell differentiation, metabolism, cell growth, survival, angiogenesis and cell motility (Bollen M et al, Crit. Rev. Biochem Mol. Biol. 2000, 35: 393; Rawadi G et al, Endocrinol 2001, 142:4673; DeFouw L et al, Microvasc Res 2001, 62:263). In addition, Phosphodiesterase 3 regulates gene expression in epithelial cells, including the expression of key adhesion molecules such as VCAM-1 (Blease K et al, Br J. Pharmacol. 1998, 124:229).

This information indicates that 161P2F10B plays a role in the growth of mammalian cells, supports cell survival and motility, and regulate gene transcription by regulating events in the nucleus. Accordingly, when 161P2F10B functions as a regulator of cell transformation, tumor formation, or as a modulator of transcription involved in activating genes associated with inflammation, tumorigenesis or proliferation, 161P2F10B is used for therapeutic, diagnostic, prognostic and/or preventative purposes. In addition, when a molecule, such as a a variant, polymorphism or SNP of 161P2F10B is expressed in cancerous tissues, such as those listed in Table I, they are used for therapeutic, diagnostic, prognostic and/or preventative purposes.

Example 45 Regulation of Transcription

The cell surface localization of 161P2F10B and ability to regulate VCAM expression indicate that 161P2F10B is effectively used as a modulator of the transcriptional regulation of eukaryotic genes. Regulation of gene expression is confirmed, e.g., by studying gene expression in cells expressing or lacking 161P2F10B. For this purpose, two types of experiments are performed.

In the first set of experiments, RNA from parental and 161P2F10B-expressing cells are extracted and hybridized to commercially available gene arrays (Clontech) (Smid-Koopman E et al. Br J Cancer. 2000. 83:246). Resting cells as well as cells treated with FBS or androgen are compared. Differentially expressed genes are identified in accordance with procedures known in the art. The differentially expressed genes are then mapped to biological pathways (Chen K et al. Thyroid. 2001. 11:41.).

In the second set of experiments, specific transcriptional pathway activation is evaluated using commercially available (Stratagene) luciferase reporter constructs including: NFkB-luc, SRE-luc, ELK1-luc, ARE-luc, p53-luc, and CRE-luc. These transcriptional reporters contain consensus binding sites for known transcription factors that lie downstream of well-characterized signal transduction pathways, and represent a good tool to ascertain pathway activation and screen for positive and negative modulators of pathway activation.

Thus, 161P2F10B plays a role in gene regulation, and it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes.

Example 46 Identification and Confirmation of Potential Signal Transduction Pathways

Many mammalian proteins have been reported to interact with signaling molecules and to participate in regulating signaling pathways. (J. Neurochem. 2001; 76:217–223). In particular, GPCRs have been reported to activate MAK cascades as well as G proteins, and been associated with the EGFR pathway in epithelial cells (Naor, Z., et al, Trends Endocrinol Metab. 2000,11:91; Vacca F et al, Cancer Res. 2000, 60:5310; Della Rocca G J et al, J. Biol. Chem. 1999, 274:13978). Using immunoprecipitation and Western blotting techniques, proteins are identified that associate with 161P2F10B and mediate signaling events. Several pathways known to play a role in cancer biology can be regulated by 161P2F10B, including phospholipid pathways such as P13K, AKT, etc, adhesion and migration pathways, including FAK, Rho, Rac-1, etc, as well as mitogenic/survival cascades such as ERK, p38, etc (Cell Growth Differ. 2000,11:279; J. Biol. Chem. 1999, 274:801; Oncogene. 2000, 19:3003, J. Cell Biol. 1997,138:913.).

To confirm that 161P2F10B directly or indirectly activates known signal transduction pathways in cells, luciferase (luc) based transcriptional reporter assays are carried out in cells expressing individual genes. These transcriptional reporters contain consensus-binding sites for known transcription factors that lie downstream of well-characterized signal transduction pathways. The reporters and examples of these associated transcription factors, signal transduction pathways, and activation stimuli are listed below.

-   -   1. NFkB-luc, NFkB/Rel; lk-kinase/SAPK; growth/apoptosis/stress     -   2. SRE-luc, SRF/TCF/ELK1; MAPK/SAPK; growth/differentiation     -   3. AP-1-luc, FOS/JUN; MAPK/SAPK/PKC; growth/apoptosis/stress     -   4. ARE-luc, androgen receptor; steroids/MAPK;         growth/differentiation/apoptosis     -   5. p53-luc, p53; SAPK; growth/differentiation/apoptosis     -   6. CRE-luc, CREB/ATF2; PKA/p38; growth/apoptosis/stress

Gene-mediated effects can be assayed in cells showing mRNA expression. Luciferase reporter plasmids can be introduced by lipid-mediated transfection (TFX-50, Promega). Luciferase activity, an indicator of relative transcriptional activity, is measured by incubation of cell extracts with luciferin substrate and luminescence of the reaction is monitored in a luminometer.

Signaling pathways activated by 161P2F10B are mapped and used for the identification and validation of therapeutic targets. When 161P2F10B is involved in cell signaling, it is used as target for diagnostic, prognostic, preventative and/or therapeutic purposes.

Example 47 Involvement in Tumor Progression

The 161P2F10B gene can contribute to the growth of cancer cells. The role of 161P2F10B in tumor growth is confirmed in a variety of primary and transfected cell lines including prostate, colon, bladder and kidney cell lines, as well as NIH 3T3 cells engineered to stably express 161P2F10B. Parental cells lacking 161P2F10B and cells expressing 161P2F10B are evaluated for cell growth using a well-documented proliferation assay (Fraser S P, Grimes J A, Djamgoz M B. Prostate. 2000;44:61, Johnson D E, Ochieng J, Evans S L. Anticancer Drugs. 1996, 7:288).

To confirm the role of 161P2F10B in the transformation process, its effect in colony forming assays is investigated. Parental NIH-3T3 cells lacking 161P2F10B are compared to N1H-3T3 cells expressing 161P2F10B, using a soft agar assay under stringent and more permissive conditions (Song Z. et al. Cancer Res. 2000;60:6730).

To confirm the role of 161P2F10B in invasion and metastasis of cancer cells, a well-established assay is used, e.g., a Transwell Insert System assay (Becton Dickinson) (Cancer Res. 1999; 59:6010). Control cells, including prostate, colon, bladder and kidney cell lines lacking 161P2F10B are compared to cells expressing 161P2F10B. Cells are loaded with the fluorescent dye, calcein, and plated in the top well of the Transwell insert coated with a basement membrane analog. Invasion is determined by fluorescence of cells in the lower chamber relative to the fluorescence of the entire cell population. Using this approach we have demonstrated that 161P2F10B induces the invasion of 3T3 cells through the basement membrane analog mabrigel (FIG. 22). As shown in FIG. 22, 3T3-neo cells that do not express 161P2F10B exhibit negligible levels of invasion though matdgel. Compared to 3T3-neo cells, 3T3-161P2F10B cells, which express abundant levels of 161P2F10B (FIG. 16), invade through matrigel and migrate to the lower chamber of the transwell system in a manner similar to that observed with cells expressing the strong protooncogene 12V-Ras.

161P2F10B can also play a role in cell cycle and apoptosis. Parental cells and cells expressing 161P2F10B are compared for differences in cell cycle regulation using a well-established BrdU assay (Abdel-Malek ZA. J Cell Physiol. 1988, 136:247). In short, cells are grown under both optimal (full serum) and limiting (low serum) conditions are labeled with BrdU and stained with anti-BrdU Ab and propidium iodide. Cells are analyzed for entry into the G1, S, and G2M phases of the cell cycle.

In contrast to normal cells, cancer cells have been shown to withstand stress, growth factor deprivation and pro-apoptotic signals, thereby providing tumors with a growth and survival advantage. The effect of stress on apoptosis is evaluated in control parental cells and cells expressing 161P2F10B, including normal and tumor prostate, colon and lung cells using standard assays methods including annexin V binding and caspase activation (Moore A, et al, Methods Cell Biol. 1998;57:265; Porter A G, Janicke R U. Cell Death Differ. 1999; 6:99). Engineered and parental cells were treated with various chemotherapeutic agents, such as etoposide, doxorubicin, kinase inhibitors such as staurosporine, DNA damaging agents such as UV, hypoxia and protein synthesis inhibitors, such as cycloheximide. Cells were stained with annexin V-FITC and cell death measured by FACS analysis. FIG. 20 shows that expression of 161P2F10B prevent the apoptosis of 3T3 cells exposed to staurosporine or UV irradiation. While 64% and 62% of 3T3-neo cells underwent apoptosis in response to staurosporine and UV irradiation, respectively, only 14% and 30% of 161P2F10B-expressing 3T3 cells died under the same conditions. Similar results were obtained in another experiment comparing the effect of staurosporine and UV irradiation on 3T3-neo cells and clonal populations of 3T3-161P2F10B cell lines (FIG. 19). As with the population of 3T3-161P2F10B, clones 3T3-161P2F10B-C and 3T3-161P2F10B-10B were resistant to staurosporine-induced cell death. Since caspase activation is a hallmark of apoptosis and serves to distinguish apoptosis from other forms of cell death, we investigated the effect of to chemotherapeutic agent and, staurosporine on the apoptosis of kidney cancer cells using caspase activation as assay read out (FIG. 21). The 769 kidney tumor cells that normally lack 161P2F10B were engineered to express the 161P2F10B protein as describe in example 8, Production of Recombinant 161P2F10B in Higher Eukaryotic Systems, above. The cells were treated with chemotherapeutic agents or staurosporine, lysed and analyzed for caspase activity. FIG. 21 shows that expression of 161P2F10B prevents caspase activation in 161P2F10B-expressing kidney cancer cells treated with doxorubicin or staurosporine. These results show that 161P2F10B imparts resistance to the chemotherapeutic drug doxorubicin and to saurosporine-induced cell death in kidney cancer cells.

A characteristic that distinguishes cancer cells from normal cells is their ability to become serum independent and survive in low serum conditions. The effect of serum deprivation on the survival of 161P2F10B expressing cells was studied using caspase activation as a read out. The fibroblast cell line Rat-1 becomes growth arrested when serum deprived, thereby mimicking normal non-transformed cells (James L, Eisenman R N. Proc Natl Acad Sci USA. 2002, 99:10429). Rat-1 cells expressing c-Myc (Rat-Myc) undergo apoptosis under serum deprivation conditions (James L, Eisenman R N. Proc Natl Acad Sci USA. 2002, 99:10429). Rat-1 and Rat-Myc cells were engineered to stably express 161P2F10B. The cells were grown in 0.1% or 10% FBS and examined for apoptosis by microscopy and caspase activity (FIGS. 17 and 18). When 161P2F10B is stably expressed in Rat-Myc cells, it inhibits Myc-induced apoptosis and reduces caspase activity to background levels. The inhibition of cell death by 161P2F10B plays a critical role in regulating tumor progression and tumor load.

When 161P2F10B plays a role in cell growth, transformation, invasion or apoptosis, it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes.

Example 48 Involvement in Angiogenesis

Angiogenesis or new capillary blood vessel formation is necessary for tumor growth (Hanahan D, Folkman J. Cell. 1996, 86:353; Folkman J. Endocrinology. 1998 139:441). Based on the effect of phsophodieseterase inhibitors on endothelial cells, and the homology of 161P2F10B to other ENPP family members, 161P2F10B plays a role in angiogenesis (DeFouw L et al, Microvasc Res 2001, 62:263). Several assays have been developed to measure angiogenesis in vitro and in vivo, such as the tissue culture assays endothelial cell tube formation and endothelial cell proliferation. Using these assays as well as in vitro neo-vascularization, the role of 161P2F10B in angiogenesis, enhancement or inhibition, is confirmed.

For example, endothelial cells engineered to express 161P2F10B are evaluated using tube formation and proliferation assays. The effect of 161P2F10B is also confirmed in animal models in vivo. For example, cells either expressing or lacking 161P2F10B are implanted subcutaneously in immunocompromised mice. Endothelial cell migration and angiogenesis are evaluated 5–15 days later using immunohistochemistry techniques. Similarly, the secreted extracellular portion of 161P2F10B can function as an angiogenic factor and enhance the proliferation and tube formation of endothelial cells. The effect of the extracellular domain of 161P2F10B on angiogenesis is supported by its similarity to other ENPPs, with biologically active secreted extracellular domain. When 161P2F10B affects angiogenesis, and it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes.

Example 49 Involvement in Protein-Protein Interactions

Several phsophodiesterases have been shown to interact with other proteins, thereby regulating gene transcription, as well as cell growth (Butt E et al, Mol Pharmacol. 1995, 47:340). Using immunoprecipitation techniques as well as two yeast hybrid systems, proteins are identified that associate with 161P2F10B. Immunoprecipitates from cells expressing 161P2F10B and cells lacking 161P2F10B are compared for specific protein-protein associations.

Studies are performed to confirm the extent of association of 161P2F10B with effector molecules, such as nuclear proteins, transcription factors, kinases, phsophates etc. Studies comparing 161P2F10B positive and 161P2F10B negative cells as well as studies comparing unstimulated/resting cells and cells treated with epithelial cell activators, such as cytokines, growth factors, androgen and anti-integrin Ab reveal unique interactions.

In addition, protein-protein interactions are confirmed using two yeast hybrid methodology (Curr Opin Chem Biol. 1999, 3:64). A vector carrying a library of proteins fused to the activation domain of a transcription factor is introduced into yeast expressing a 161P2F10B-DNA-binding domain fusion protein and a reporter construct. Protein-protein interaction is detected by colorimetric reporter activity. Specific association with effector molecules and transcription factors directs one of skill to the mode of action of 161P2F10B, and thus identifies therapeutic, prognostic, preventative and/or diagnostic targets for cancer. This and similar assays are also used to identify and screen for small molecules that interact with 161P2F10B. Thus it is found that 161P2F10B associates with proteins and small molecules. Accordingly, 161P2F10Band these proteins and small molecules are used for diagnostic, prognostic, preventative and/or therapeutic purposes.

Example 50 Involvement in Cell Adhesion

Cell adhesion plays a critical role in tissue colonization and metastasis. 161P2F10B can participate in cellular organization, and as a consequence cell adhesion and motility. To confirm that 161P2F10B regulates cell adhesion, control cells lacking 161P2F10B are compared to cells expressing 161P2F10B, using techniques previously described (see, e.g., Haieretal,Br. J. Cancer. 1999, 80:1867; LehrandPienta, J. Natl. Cancer Inst. 1998, 90:118). Briefly, in one embodiment, cells labeled with a fluorescent indicator, such as calcein, are incubated on tissue culture wells coated with media alone or with matrix proteins. Adherent cells are detected by fluorimetric analysis and percent adhesion is calculated. In another embodiment, cells lacking or expressing 161P2F10B are analyzed for their ability to mediate cell-cell adhesion using similar experimental techniques as described above. Both of these experimental systems are used to identify proteins, antibodies and/or small molecules that modulate cell adhesion to extracellular matrix and cell-cell interaction. Cell adhesion plays a critical role in tumor growth, progression, and, colonization, and 161P2F10B is involved in these processes. Thus, it serves as a diagnostic, prognostic, preventative and/or therapeutic modality.

Example 51 Phosphodiesterase Activity of 161P2F10B Expressing Recombinant Cell Lines

In order to delineate the function 161P2F10B, several cell lines that lack 161P2F10B were transduced with 161P2F10B-encoding retovirus as described in example 8, Production of Recombinant 161P2F10B in Higher Eukaryotic Systems, above. Cell lines were characterized for 161P2F10B cell surface expression by FACS analysis (FIGS. 28, 29, 30, and 16). cDNA was stably introduced into the fibroblast lines NIH 3T3 and Rat-1, myeloma NSO cells, and kidney cancer CaKi cells. The cells were immunostained with anti-CD203c mAb and analyzed by flow cytometry. FIGS. 28, 29, 30, and 16 show that while parental cells fail to express 161P2F10B, engineered lines demonstrate abundant expression of 161P2F10B on their cell surface. Expression of 161P2F10B in engineered cells was compared to that in UT7, a cell line that expresses 161P2F10B endogenously (FIG. 28). Our results show that engineered Rat-T and 3T3 cells express 161P2F10B at levels comparable to UT7 cells.

Since 161P2F10B is identical to the ecto-enzyme ENPP3 phosphodieterase, and members of the ENPP family possess pyrophosphatase activities, the recombinant cell lines were also characterized for phosphodiesterase activity (FIGS. 28, 29, 30, and 16). Control and 161P2F10B-expressing cells were lysates or intact cells were incubated for at 37 degrees in 20 mM Tris/HCL, pH 9.6 containing 5 mM MgCl₂ and 1 mM p-nitrophenyl thymidine-5′-L-monophosphate. The reaction was terminated by the addition of 0.1 N NaOH and the reaction product quantified by reading absorbance at 410 nm. FIGS. 28, 29, 30, and 16 show that 161P2F10B expression parallels phosphodiesterase activity. Using CaKi cells expressing either wild type or mutant 161P2F10B, we show that mutation of T205 inhibits phosphodiesterase activity (FIG. 30). When 161P2F10B shows phosphodiesterase activity, it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes.

In addition to phosphodiesterase activity, members of the ENPP family exhibit lysophospholipase D (lysoPLD) activity (Umezu-Goto M et al, J. Cell Biol. 2002, 158: 227). ENPP-2 (aka autotoxin) in particular was found to act on lysophosphatidylcholine (LPC) to generate lysophosphatidic acid (LPA) (Umezu-Goto M et al, J. Cell Biol. 2002, 158: 227; Tokumura A et al, J boil. Chem 2002, 277:39436). LPA is involved in various biological functions associated with tumor development, including cell proliferation and invasion (Gschwind A, Prenzel N, Ullrich A. Cancer Res. 2002, 62:6329). Based on the homology of 161P1F10B to other ENPP family members, 161P2F10B has lysoPLD activity. The lysoPLD activity of 161P2F10B expressing cells is compared to cells lacking 161P2F10B using a standard choline release assay. In short, cell lysates are incubated with LPC for 1 hr at 37° C. Liberated choline is detected by fluoremetry following the addition of choline oxidase. When 161P2F10B shows lysoPLD activity, it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes.

Example 52 RNA Interference (RNAi)

Several methods of reducing or abolishing the expression of specific genes have been used for confirming the importance of said genes in tumor growth and progression. These methods include antisense oligonucleotides, morpholino, ribozyme, etc that function in a sequence specific manner to prevent gene transcription or translation. More recently, RNA interference by duplexes of short nucleotide RNAs has been shown to inhibit gene expression in a sequence specific manner in mammalian cells (Elbashir S et al, Nature 2001, 411:494). RNA interference (RNAi) makes use of sequence specific double stranded RNA known as small interfering RNAs (siRNAs) to prevent gene expression. Small interfering RNA (siRNA) are transfected into mammalian cells and thereby mediate sequence specific mRNA degradation. (Elbashir, et al, Nature, 2001; 411: 494). Similarly, siRNA have been used to generate stable vector systems that can be delivered in vitro and in vivo to mammalian cells, thereby providing therapeutic use for siRNAs (Lee N et al, Nature Biotechnol 2002, 19:500). Several siRNAs can be used to modulate the expression of 161P2F10B in mammalian cells, including for example the following siRNA oligonucleotide sequences:

161P2F10B (1) target: GMUCUACGUUGACUUUAG (corresponding to nucleotides 4–23 of 161P2F10B ORF) (SEQ ID NO: 39)

The sense strand of 161P2F10B (1) can labeled at 3′ with fluorescein, 6-FAM (ABS 494 nm, EMM 525 nm, green) for easy detection. The siRNA is dissolved in RNA-free sterile buffer (100 mM KOAc, 30 mM HEPES KOH, 2 mM MOAc, at pH 7.4) to make 20 μM stock (200×). The siRNa is transfected into various normal and tumor cells, including UT7, 3T3-161P2F10B, CaKi-161P2F10B and Rat-161P2F10B cells. Control, non-specific oligonucleotide is used as a control to rule out any non-specific effect of 161P2F10B siRNA oligonucleotides.

Protein expression is determined 24–48 hours after transfection by immunostaining followed by flow cytometry. In addition, confirmation of altered gene expression is performed by Western blotting. Cells transfected with control or 161P2F10B-specific siRNAi are compared using functional assays described above, including invasion, proliferation, colony formation and response to apoptotic stimuli. Therefore, the RNA oligonucleotide sequences are used to assess how modulating the expression of a 161P2F10B gene affects function of cancer cells and/or tissues.

Accordingly, the RNA oligonucleotide sequences are used in therapeutic and prophylactic applications.

Example 53 Generation of Antibodies to 161P2F10B Using Peptide Encoding the Caytalytic Domain of 161P2F10B as the Immunogen

In one embodiment peptides of 22 amino acids encompassing the 161P2F10B catalytic domain (Threonine (T) at position 205), CGIHSKYMRAMYPTKTFPNHYT (SEQ ID NO: 40) were generated. These were, synthesized and the peptides were coupled to KLH through the N-terminal cysteine residue.

Balb/c mice were immunized intraperitoneally (i.p.) with 10 μg of peptide every 2 weeks over a 4 week period. The initial immunization was given i.p. in Complete Freunds Adjuvant (CFA) and the subsequent two immunizations were given i.p. in Incomplete Freunds Adjuvant (IFA).

To determine the specificity of the response following immunization, mice were bled 10 days after the final immunization. Reactivity was determined by Enzyme Linked Immunosorbent Assay (ELISA) using non-KLH conjugated (free) peptide as a target. Mice with the highest Uters were given a final boost of 10 μg peptide in PBS and sacrificed for fusion 3 days later. Spleen cells from the immunized mice were fused with mouse Sp2/0 myeloma cells using PEG 1500 according to standard protocols (Kohler et al, Eur. J. Immunol 6: 511 (1976)). Fused cells were plated in 10 96 well microtiter plates and hybridomas were selected using HAT media supplement. Supernatants from fusion wells were screened 10–17 days later by ELISA against 161P2F10B peptide, and clones were then checked for the ability of the monoclonal antibody to recognize cell membrane 161P2F10B by FACS on 161P2F10B expressing Rat-1 cells.

Example 54 Generation of Antibodies to 161P2F10B Using Protein Encoding the Whole Extra Cellular Domain (aa 1–975) of 161P2F10B as the Immunogen

In one embodiment the whole extra cellular domain of 161P2F10B fused at the C′ terminal with 6 Histidines (6-His for purification was purified hor use as an immunogen.

Balb/c mice were immunized intraperitoneally (i.p.) with 10 μg of protein every 2 weeks over a 4 week period. The initial immunization was given i.p. in Complete Freunds Adjuvant (CFA) and the subsequent two immunizations were given i.p. in Incomplete Freunds Adjuvant (IFA).

To determine the specificity of the response following immunization, mice were bled 10 days after the final immunization. Reactivity was determined by Enzyme Linked Immunosorbent Assay (ELISA) using purified protein as a screening agent.

Mice with the highest titers were given a final boost of 10 μg protein in PBS and sacrificed for fusion 3 days later. Spleen cells from the immunized mice were fused with mouse Sp2/0 myeloma cells using PEG 1500 according to standard protocols (Kohler et al, Eur. J. Immunol 6: 511 (1976)). Fused cells were plated in 10 96 well microtiter plates and hybridomas were selected using HAT media supplement. Supernatants from fusion wells were screened 10–17 days later by ELISA against 161P2F10B protein, and clones were then checked for the ability of the monoclonal antibody to recognize cell membrane 161P2F10B by FACS on 161P2F10 expressing Rat-1 cells.

Example 55 Generation Mabs to 161P2F10B Using DNA Immunization with a Vector Encoding 161P2F10B Fused at the C′ Terminus with Human IgG Fc

In another embodiment, a vector was constructed that encodes the 975 amino acids of the 161P2F10 extra cellular domain fused at the C-terminus to the human immunoglobulin G1 (IgG1 Fc (hinge, CH2, CH3 regions). This construct was used in a DNA based immunization strategy.

Balb/c mice were immunized intra-dermally (ID) at the base of their tail. Three immunizations were given to each mouse of 100 μg of DNA in PBS over a two-week period. To increase the immune response, each mouse was given an i.p. boost of 2 μg of 161P2F10B-Fc protein in tissue culture media 10 days after the final DNA immunization. Bleeds were collected 10 days after the final immunization and reactivity in the sera to the middle loop of 161 P2F10B was tested by ELISA using 161P2F10B-Fc fusion protein as a target (test 1). In parallel the sera were also tested on an unrelated human Fc fusion protein (test 2). Specific reactivity to the 161 P2F10B portion of the fusion protein was indicated. All mice were sacrificed and fusions and hybridoma selection was carried out as described in Example 54. Hybridoma supernatants were screened 10–17 days later by ELISA using 161P2F10B-Fc protein as target. 161P2F10B-Fc positives were subsequently cross-screened on irrelevant Fc proteins to identify 161P2F10 specific clones. Monoclonal antibodies were tested for specificity and reactivity to cell surface 161p2F10B using recombinant Rat 1 cells. Several antibodies were identified this way including X41(4)6, X41(3)15, X41(3)17, X41(3)29, X41(3)37 and X41(3)50. These antibodies or binding region thereof secreted by a hybridoma entitled X41(3)15/29/37, X41(4)6, X41(3)50 were deposited with the Anerican Type Culture Collection (ATCC; 10801 University Blvd., Manassas, Va. 20110-2209 USA) on Nov. 7, 2002 and assigned as Patent Deposit Designation No. PTA-4791, Patent Deposit Designation No. PTA-4794, Patent Deposit Designation No. PTA-4792. and Patent Deposit Desianation No. PTA-4793 (respectively). FAGS data for these monoclonal antibodies is shown on (FIG. 40).

Example 56 Generation of Mabs to 161P2F10B Using DNA Immunization with a Vector Encoding 161P2F10B fused at the C′ Terminus with the myc His Tag

In another embodiment, a vector was constructed that encodes the 975 amino acids of the 161P2F10 extra cellular domain fused at the C-terminus to the myc-His tag. This construct was used in a DNA based immunization strategy.

Balb/c mice were immunized intra-dermally (ID) at the base of their tail. Three immunizations were given to each mouse of 100 μg of DNA in PBS over a two-week period. To increase the immune response, each mouse was given an i.p. boost of 2 μg of 161P2F10B-Fcprotein in tissue culture media 10 days after the final DNA immunization. Bleeds were collected 10 days after the final immunization and reactivity in the sera to the middle loop of 161P2F10B was tested by ELISA using 161P2F10B-Fc fusion protein as a target (test 1). In parallel the sera were also tested on an unrelated human Fc fusion protein (test 2). Specific reactivity to the 161P2F10B portion of the fusion protein was indicated.

All mice were sacrificed and fusions and hybridoma selection was carried out as described in Example 11. Hybridoma supernatants were screened 10–17 days later by ELISA using 161P2F10B-Fc protein as target. 161P2F10B-Fc positives were subsequently cross-screened on irrelevant Fc proteins to identify 161P2F10 specific clones. Monoclonal antibodies were tested for specificity and reactivity to cell surface 161p2F10B using recombinant Rat 1 cells.

Example 57 Generation of Monoclonal Antibodies Specific for 161P2F10B using UT7 Cells Endogenously Expressing 161P2F10B

It has been reported in the literature that antibodies to 161P2F10B can be made by immunization with the human erythro-megakaryoblastic cell line UT-7 cultured with IL3 (Buhring et. al. Blood 94(7): 2343. 1999). Antibodies described in this publication are available commercially and have been used as controls in the invention described here. In another embodiment, mice were immunized intraperitoneally with UT-7 cells, 106 cells per immunization. A total of 5 immunizations were given approximately 2 weeks apart with the final injection being given three days befor mice were sacrificed for fusions. Mice were bled 10 days after the third injection and the 161P2F10B specific titer of the sera was determined by ELISA using 161P2F10 as a screening agent. Mice with high titers were then used for fusions as described in Example 11. Monoclonal antibodies generated in this way were selected by ELISA and their ability to recognize cells surface 161P2F10B was confirmed by FACS on Rat 1 cells expressing 161P2F10B.

Example 58 Generation of Monoclonal Antibodies Specific for 161P2F10B Using the Recombinant Cell Line 3T3 Expressing 161P2F10B

In another embodiment, mice were immunized intea-peritoneally with 3T3 cells expressing 161P2F10B, 10⁶ cells per immunization. A total of 5 immunizations were given approximately 2 weeks apart with the final injection being given three days before mice were sacrificed for fusions. Mice were bled 10 days after the third injection and the 161P2F10B specific titer of the sera was determined by ELISA using 161P2F10 as a screening agent. Mice with high titers were then used for fusions as described in Example 11. Monoclonal antibodies generated in this way were selected by ELISA and their ability to recognize cells surface 161P2F10B was confirmed by FACS on Rat 1 cells expressing 161P2F10B.

Example 59 Generation of Monoclonal Antibodies Specific for 161P2F10B Using the Recombinant Cell Line Rat 1 Expressing 161P2F10B

In another embodiment mice were immunized with Rat-i cells expressing 161P2F10B, Mice were then used for fusions as described in Example 11. Monoclonal antibodies generated in this way were selected by ELISA and their ability to recognize cells surface 161P2F10B was confirmed by FACS on Rat 1 cells expressing 161P2F10B.

Example 60 Detection of 161P2F10B Protein in Kidney Cancer Patient Specimens

To confirm the expression of 161P2F10B protein, kidney cancer specimens were obtained from kidney cancer patients, and stained using the commercially available antibody 97A6 specific for ENPP3 protein (also called anti-CD203c) (Immunotech, Marseilles, France). Briefly, frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes. The sections were then incubated with PE-labeled mouse monoclonal anti-ENPP3 antibody for 3 hours (FIGS. 24A–C), or isotype control antibody (FIGS. 44G–I). The slides were washed three times in buffer, and either analyzed by fluorescence microscopy (FIGS. 44A, B and C), or further incubated with DAKO EnVision+™ peroxidase-conjugated goat anti-mouse secondary antibody (DAKO Corporation, Carpenteria, Calif.) for 1 hour (FIGS. 44D, E, and F FIGS. 24A–C). The sections were then washed in buffer, developed using the DAB kit (SIGMA Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy (FIGS. 44D, E and F). The results showed strong expression of 161P2F10B in the renal carcinoma patient tissue (FIGS. 44A and D) and the kidney cancer metastasis to lymph node tissue (FIGS. 44C and F), but weakly in normal kidney (FIGS. 44B and E). The expression was detected mostly around the cell periphery in renal clear cell carcinoma (FIGS. 44A and D, FIGS. 24A and B) and was strongly expressed throughout the cells with an apparent predisposition towards the cell periphery in renal papillary carcinoma (FIG. 24C) indicating that 161P2F10B is membrane associated in kidney cancer tissues. The weak expression detected in normal kidney was localized to the kidney tubules. The sections stained with the isotype control antibody were negative showing the specificity of the anti-ENPP3 antibody (FIGS. 44G–I). Kidney cancer specimens were obtained from patients with different types of renal tumor including renal clear cell carcinoma; papillary cell carcinoma; renal cell carcinoma, chromophobe type; transitional cell carcinoma and oncocytoma and were stained for 161P2F10B using the commercially available antibody 97A6 specific for ENPP3 protein (also called anti-CD203c) (Immunotech, Marseilles, France). All tissue specimens for renal clear cell carcinoma and papillary cell carcinoma were positive for 161P2F10B (Table LIX).

FIG. 45 shows expression of 161P2F10B in human patient cancers by Western blot analysis. Cell lysates from kidney cancer tissues (KiCa), kidney cancer metastasis to lymph node (KiCa Met), as well as normal kidney (NK) were subjected to western analysis using an anti-161P2F10B mouse monoclonal antibody. Briefly, tissues (˜25 μg total protein) were solubilized in SDS-PAGE sample buffer and separated on a 10–20% SDS-PAGE gel and transferred to nitrocellulose. Blots were blocked in Tris-buffered saline (TBS)+3% non-fat milk and then probed with purified anti-161P2F10B antibody in TBS+0.15% Tween-20+1% milk. Blots were then washed and incubated with a 1:4,000 dilution of anti-mouse IgG-HRP conjugated secondary antibody. Following washing, anti-161P2F10B immunoreactive bands were developed and visualized by enhanced chemiluminescence and exposure to autoradiographic film. The specific anti-161P2F10B immunoreactive bands represent a monomeric form of the 161P2F10B protein, which runs at approximately 130 kDa. These results demonstrate that 161P2F10B is useful as a diagnostic and therapeutic target for kidney cancers, metastatic cancers and other human cancers that express this protein.

The strong expression of 161P2F10B in kidney cancer tissues and its restricted expression in normal kidney as well as its membrane localization show that 161P2F10B is a target, e.g., for kidney cancer diagnosis and therapy. The expression detected in kidney cancer metastatic tissue indicates that 161P2F10B is also a target for metastatic disease. As disclosed herein, Western blot and immunohistochemical analysis of kidney cancer tissues and kidney cancer xenografts with mAb 97A6 showed strong extensive staining of ENPP3 in clear cell kidney carcinoma but significantly lower or undetectable levels in normal kidney (FIGS. 44, 45, 46, and 24). Detection of 161P2F10B (ENPP3) in high grade clear cell carcinoma and in metastatic disease.

Example 61 Detection of 161P2F10B Protein in Colon Cancer Patient Specimens

Tissue specimens of colon adenocarcinoma were obtained from nine different colon cancer patients. Frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes. The sections were then incubated with mouse monoclonal anti-ENPP3 antibody (Coulter-Immunotech, Marseilles, France) for 3 hours. The slides were washed three times in buffer, and further incubated with DAKO EnVision+™ peroxidase-conjugated goat anti-mouse secondary antibody (DAKO Corporation, Carpenteria, Calif.) for 1 hour. The sections were then washed in buffer, developed using the DAB kit (SIGMA Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy. The results showed strong expression of 161P2F10B in two of the nine colon cancer patient tissues, one of which is illustrated (FIG. 26). 161P2F10B was most strongly expressed on the tumor cells with a luminal cell surface but was also expressed throughout all the tumor tissue.

Example 62 Detection of 161P2F10B Protein by Immunohistochemistry in a Prostate Cancer Patient Specimens

Tissue specimens of prostate adenocarcinoma were obtained from eight different prostate cancer patients. Frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes. The sections were then incubated with mouse monoclonal anti-ENPP3 antibody (Coulter-Immunotech, Marseilles, France) for 3 hours. The slides were washed three times in buffer, and further incubated with DAKO EnVision+™ peroxidase-conjugated goat anti-mouse secondary antibody (DAKO Corporation, Carpenteria, Calif.) for 1 hour. The sections were then washed in buffer, developed using the DAB kit (SIGMA Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy. The results showed expression of 161P2F10B in six of the eight prostate cancer patient tissues, one of which is illustrated (FIG. 25). 161P2F10B was expressed on the tumor cells with an apparent proclivity towards the luminal cell surface.

Example 63 Detection of 161P2F10B Protein by Immunohistochemistry in Normal Tissue Specimens

Normal tissue specimens from a number of organs were obtained either from patients undergoing surgery or from autopsy. Frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes. The sections were then incubated with mouse monoclonal anti-ENPP3 antibody (Coulter-Immunotech, Marseilles, France) for 3 hours. The slides were washed three times in buffer, and further incubated with DAKO EnVision+™ peroxidase-conjugated goat anti-mouse secondary antibody (DAKO Corporation, Carpenteria, Calif.) for 1 hour. The sections were then washed in buffer, developed using the DAB kit (SIGMA Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy. The results showed weak expression of 161P2F10B in some of the tubules in all of the kidney specimens and weak staining of some glandular epithelium in half of the prostate tissues. There was no expression of 161P2F10B in any of the other normal tissues studied except for expression in a very few cells within one lung, one bladder and two colon samples which could be mast cells (TABLE LX). As disclosed herein, Western blot and immunohistochemical analysis of kidney cancer tissues and kidney cancer xenografts with mAb 97A6 showed strong extensive staining of ENPP3 in clear cell kidney carcinoma but significantly lower or undetectable levels in normal kidney (FIGS. 44, 45, 46, and 24). Detection of 161P2F10B (ENPP3) in high grade clear cell carcinoma and in metastatic disease.

Example 64 Detection by Immunohistochemistry of 161P2F10B Protein Expression in Kidney Clear Cell Cancer Patient Specimens by Specific Binding of Mouse Monoclonal Antibodies

Renal clear cell carcinoma tissue and its matched normal adjacent were obtained from a kidney cancer patient. Frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes. The sections were then incubated either mouse monoclonal anti-ENPP3 antibody (Coulter-Immunotech, Marseilles, France) for 3 hours (FIG. 27 panels A, D), or mouse monoclonal antibody X41(3)50 (FIG. 27 panels B, E), or mouse monoclonal antibody X41(3)37 (FIG. 27 panels C, F). The slides were washed three times in buffer and further incubated with DAKO EnVision+™ peroxidase-conjugated goat anti-mouse secondary antibody (DAKO Corporation, Carpentena, Calif.) for 1 hour. The sections were then washed in buffer, developed using the DAB kit (SIGMA Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy (FIG. 27 panels A–F). The results showed strong expression of 161P2F10B in the renal clear cell carcinoma patient tissue (FIG. 27 panels A–C), but weakly in normal kidney (FIG. 27 panels D–F). The expression was predominantly around the cell periphery indicating that 161P2F10B is membrane associated in kidney cancer tissues. The weak expression detected in normal kidney was localized to the kidney proximal tubules. As disclosed herein, Western blot and immunohistochemical analysis of kidney cancer tissues and kidney cancer xenografts with mAb 97A6 showed strong extensive staining of ENPP3 in clear cell kidney carcinoma but significantly lower or undetectable levels in normal kidney (FIGS. 44, 45, 46, and 24). Detection of 161P2F10B (ENPP3) in high grade clear cell carcinoma and in metastatic disease.

Example 65 Characteristics and Utility of Anti-161P2F10b MAbs

Using a variety of immunization strategies as described in Example 11, a panel of MAbs that specifically bind 161P2F10b protein was generated. The characteristics of this panel is summarized in FIG. 39 These antibodies specifically bind with high affinity to 161P2F10b on the surface of endogenously-expressing and recombinant cell lines as determined by flow cytometry (FIGS. 28 and 40). Upon engagement of surface 161P2F10b, these MAbs mediate internalization of the MAb-protein complex (FIGS. 33, 34, and 35). These MAbs are thus useful as a specific targeting modality for toxin-conjugates, as exemplified by the growth inhibition and induction of apoptosis of Caki-161P2F10b cells by MAb X41.50 with a saporin toxin-conjugated secondary Ab (FIG. 36). Treatment of 161P2F10-expressing cancerous cells with the naked MAb also has a therapeutic effect in vivo as exemplified by the inhibition of UGK3 tumor formation in SCID mice injected with MAb X41.50 (FIG. 23).

161P2F10b encodes phosphodiesterase enzymatic activity that is easily monitored both in recombinant purified protein (FIG. 31) and on cells (FIG. 32). The relevance of the enzymatic activity to the function of 161P2F10b may be monitored by utilization of mutants that disrupt this activity (FIG. 30). Engagement of 161P2F10b with MAbs may alter, disrupt, block, or downregulate 161P2F10 enzymatic activity, which may serve as a potential therapeutic mechanism for targeting 161P2F10b-expressing cancers and diseased tissues. Engagement of cell surface 161P2F10b cells with a subset of the MAbs listed in FIG. 39 does mediate internalization and marked downregulation of cell surface enzymatic activity (FIGS. 37 and 38) thus demonstrating the utility of the MAbs for disrupting the function of 161P2F10b in cells and tissues.

161P2F10b protein and the MAbs that bind it are useful in the diagnosis of 161P2F10b-expressing cancer and diseased tissues. Immunohistochemical analysis of the panel of MAbs, as summarized in FIG. 39, specifically stain (to varying degrees) a variety of kidney cancer samples with little to no staining of adjacent normal tissues. These MAbs are thus useful as diagnostic reagents for a variety of 161P2F10b-expressing cancers by immunohistochemistry and are potentially useful as imaging reagents in patients. In addition, the MAbs were used (specifically X48.54 and X41.29, but others that do not compete for the same epitope are also used) to demonstrate the shedding and/or secretion of the protein from 161P2F10b-expressing cancer cells and tissues (FIGS. 42 and 43). This supports the utility of 161P2F10b as a serum and/or urine diagnostic marker and the MAbs as reagents to quantitatively measure serum and/or urine concentrations of 161P2F10b protein.

Throughout this application, various website data content, publications, patent applications and patents are referenced. (Websites are referenced by their Uniform Resource Locator, or URL, addresses on the World Wide Web.) The disclosures of each of these references are hereby incorporated by reference herein in their entireties.

The present invention is not to be limited in scope by the embodiments disclosed herein, which are intended as single illustrations of individual aspects of the invention, and any that are functionally equivalent are within the scope of the invention. Various modifications to the models and methods of the invention, in addition to those described herein, will become apparent to those skilled in the art from the foregoing description and teachings, and are similarly intended to fall within the scope of the invention. Such modifications or other embodiments can be practiced without departing from the true scope and spirit of the invention.

Tables:

TABLE I Tissues that Express 161P2F10B: a. Exemplary Normal Tissues: Prostate Kidney b. Malignant Tissues Kidney Uterus Pancreas Prostate Colon Lung Bone Lymphoma Breast Ovary

TABLE II Amino Acid Abbreviations SINGLE LETTER THREE LETTER FULL NAME F Phe phenylalanine L Leu leucine S Ser serine Y Tyr tyrosine C Cys cysteine W Trp tryptophan P Pro proline H His histidine Q Gln glutamine R Arg arginine I Ile isoleucine M Met methionine T Thr threonine N Asn asparagine K Lys lysine V Val valine A Ala alanine D Asp aspartic acid E Glu glutamic acid G Gly glycine

TABLE III Amino Acid Substitution Matrix Adapted from the GCG Software 9.0 BLOSUM62 amino acid substitution matrix (block substitution matrix). The higher the value, the more likely a substitution is found in related, natural proteins. A C D E F G H I K L M N P Q R S T V W Y . 4 0 −2 −1 −2 0 −2 −1 −1 −1 −1 −2 −1 −1 −1 1 0 0 −3 −2 A 9 −3 −4 −2 −3 −3 −1 −3 −1 −1 −3 −3 −3 −3 −1 −1 −1 −2 −2 C 6 2 −3 −1 −1 −3 −1 −4 −3 1 −1 0 −2 0 −1 −3 −4 −3 D 5 −3 −2 0 −3 1 −3 −2 0 −1 2 0 0 −1 −2 −3 −2 E 6 −3 −1 0 −3 0 0 −3 −4 −3 −3 −2 −2 −1 1 3 F 6 −2 −4 −2 −4 −3 0 −2 −2 −2 0 −2 −3 −2 −3 G 8 −3 −1 −3 −2 1 −2 0 0 −1 −2 −3 −2 2 H 4 −3 2 1 −3 −3 −3 −3 −2 −1 3 −3 −1 I 5 −2 −1 0 −1 1 2 0 −1 −2 −3 −2 K 4 2 −3 −3 −2 −2 −2 −1 1 −2 −1 L 5 −2 −2 0 −1 −1 −1 1 −1 −1 M 6 −2 0 0 1 0 −3 −4 −2 N 7 −1 −2 −1 −1 −2 −4 −3 P 5 1 0 −1 −2 −2 −1 Q 5 −1 −1 −3 −3 −2 R 4 1 −2 −3 −2 S 5 0 −2 −2 T 4 −3 −1 V 11 2 W 7 Y

TABLE IV HLA Class I/II Motifs/Supermotifs TABLE IV (A): HLA Class I Supermotifs/Motifs POSITION C Terminus POSITION POSITION (Primary 2 (Primary Anchor) 3 (Primary Anchor) Anchor) SUPER- MOTIF A1 TI LVMS FWY A2 LIVM ATQ IV MATL A3 VSMA TLI RK A24 YF WIVLMT FI YWLM B7 P VILF MWYA B27 RHK FYL WMIVA B44 ED FWYLIMVA B58 ATS FWY LIVMA B62 QL IVMP FWY MIVLA MOTIFS A1 TSM Y A1 DEAS Y A2.1 LM VQIAT V LIMAT A3 LMVISATF CGD KYR HFA A11 VTMLISAGN CDF K RYH A24 YFW M FLIW A*3101 MVT ALIS R K A*3301 MVALF IST RK A*6801 AVT MSLI RK B*0702 P LMF WYAIV B*3501 P LMFWY IVA B51 P LIVF WYAM B*5301 P IMFWY ALV B*5401 P ATIV LMFWY Bolded residues are preferred, italicized residues are less preferred: A peptide is considered motif-bearing if it has primary anchors at each primary anchor position for a motif or supermotif as specified in the above table.

TABLE IV (B) HLA Class II Supermotif 1 6 9 W, F, Y, V, .I, L A, V, I, L, P, C, S, T A, V, I, L, C, S, T, M, Y

TABLE IV (C) HLA Class II Motifs MOTIFS 1° anchor 1 2 3 4 5 1° anchor 6 7 8 9 DR4 preferred FMYLIVW M T I VSTCPALIM MH MH deleterious W R WDE DR1 preferred MFLIVWY PAMQ VMATSPLIC M AVM deleterious C CH FD CWD GDE D DR7 preferred MFLIVWY M W A IVMSACTPL M IV deleterious C G GRD N G DR3 MOTIFS 1° anchor 1 2 3 1° anchor 4 5 1° anchor 6 Motif a preferred LIVMFY D Motif b preferred LIVMFAY DNQEST KRH DR Supermotif MFLIVWY VMSTACPLI Italicized residues indicate less preferred or “tolerated” residues

TABLE IV (D) HLA Class I Supermotifs SUPER- MOTIFS POSITION: 1 2 3 4 5 6 7 8 C-terminus A1 1° Anchor 1° Anchor TILVMS FWY A2 1° Anchor 1° Anchor LIVMATQ LIVMAT A3 Preferred 1° Anchor YFW YFW YFW P 1° Anchor VSMATLI (4/5) (3/5) (4/5) (4/5) RK deleterious DE (3/5); DE P (5/5) (4/5) A24 1° Anchor 1° Anchor YFWIVLMT FIYWLM B7 Preferred FWY (5/5) 1° Anchor FWY FWY 1° Anchor LIVM (3/5) P (4/5) (3/5) VILFMWYA deleterious DE (3/5); DE G QN DE P (5/5); (3/5) (4/5) (4/5) (4/5) G (4/5); A (3/5); QN (3/5) B27 1° Anchor 1° Anchor RHK FYLWMIVA B44 1° Anchor 1° Anchor ED FWYLIMVA B58 1° Anchor 1° Anchor ATS FWYLIVMA B62 1° Anchor 1° Anchor QLIVMP FWYMIVLA Italicized residues indicate less preferred or “tolerated” residues

TABLE IV (E) HLA Class I Motifs 9 or C- POSITION 1 2 3 4 5 6 7 8 C-terminus terminus A1 preferred GFYW 1° Anchor DEA YFW P DEQN YFW 1° Anchor 9-mer STM Y deleterious DE RHKLIVMP A G A A1 preferred GRHK ASTCLIVM 1° Anchor GSTC ASTC LIVM DE 1° Anchor 9-mer DEAS Y deleterious A RHKDEPYFW DE PQN RHK PG GP A1 preferred YFW 1° Anchor DEAQN A YFWQN PASTC GDE P 1° Anchor 10- STM Y mer deleterious GP RHKGLIVM DE RHK QNA RHKYFW RHK A A1 preferred YFW STCLIVM 1° Anchor A YFW PG G YFW 1° Anchor 10- DEAS Y mer deleterious RHK RHKDEPYFW P G PRHK QN A2.1 preferred YFW 1° Anchor YFW STC YFW A P 1° Anchor 9-mer LMIVQAT VLIMAT deleterious DEP DERKH RKH DERKH C- POSITION: 1 2 3 4 5 6 7 8 9 Terminus A2.1 preferred AYFW 1° Anchor LVIM G G FYWL 1° Anchor 10- LMIVQAT VIM VLIMAT mer deleterious DEP DE RKHA P RKH DERK RKH H A3 preferred RHK 1° Anchor YFW PRHKYF A YFW P 1° Anchor LMVISATFCGD W KYRHFA deleterious DEP DE A11 preferred A 1° Anchor YFW YFW A YFW YFW P 1° Anchor VTLMISAGNCD KRYH F deleterious DEP A G A24 preferred YFWRHK 1° Anchor STC YFW YFW 1° Anchor 9-mer YFWM FLIW deleterious DEG DE G QNP DERH G AQN K A24 Preferred 1° Anchor P YFWP P 1° Anchor 10- YFWM FLIW mer Deleterious GDE QN RHK DE A QN DEA A310 Preferred RHK 1° Anchor YFW P YFW YFW AP 1° Anchor 1 MVTALIS RK Deleterious DEP DE ADE DE DE DE A330 Preferred 1° Anchor YFW AYFW 1° Anchor 1 MVALFIST RK Deleterious GP DE A680 Preferred YFWSTC 1° Anchor YFWLIV YFW P 1° Anchor 1 AVTMSLI M RK deleterious GP DEG RHK A B070 Preferred RHKFWY 1° Anchor RHK RHK RHK RHK PA 1° Anchor 2 P LMFWYAI V deleterious DEQNP DEP DE DE GDE QN DE 9 or C- POSITION 1 2 3 4 5 6 7 8 C-terminus terminus A1 preferred GFYW 1° Anchor DEA YFW P DEQN YFW 1° Anchor 9-mer STM Y deleterious DE RHKLIVMP A G A A1 preferred GRHK ASTCLIVM 1° Anchor GSTC ASTC LIVM DE 1° Anchor 9-mer DEAS Y deleterious A RHKDEPYFW DE PQN RHK PG GP B350 Preferred FWYLIVM 1° Anchor FWY FWY 1° Anchor 1 P LMFWYIV A deleterious AGP G G B51 Preferred LIVMFWY 1° Anchor FWY STC FWY G FWY 1° Anchor P LIVFWYA M deleterious AGPDER DE G DEQN GDE HKSTC B530 preferred LIVMFWY 1° Anchor FWY STC FWY LIVMFW FWY 1° Anchor 1 P Y IMFWYAL V deleterious AGPQN G RHKQN DE B540 preferred FWY 1° Anchor FWYLIVM LIVM ALIVM FWYA 1° Anchor 1 P P ATIVLMF WY deleterious GPQNDE GDESTC RHKDE DE QNDGE DE

TABLE IV (F) Summary of HLA-supertypes Overall phenotypic frequencies of HLA-supertypes in different ethnic populations Specificity Phenotypic frequency Supertype Position 2 C-Terminus Caucasian N.A. Black Japanese Chinese Hispanic Average B7 P AILMVFWY 43.2 55.1 57.1 43.0 49.3 49.5 A3 AILMVST RK 37.5 42.1 45.8 52.7 43.1 44.2 A2 AILMVT AILMVT 45.8 39.0 42.4 45.9 43.0 42.2 A24 YF (WIVLMT) FI (YWLM) 23.9 38.9 58.6 40.1 38.3 40.0 B44 E (D) FWYLIMVA 43.0 21.2 42.9 39.1 39.0 37.0 A1 TI (LVMS) FWY 47.1 16.1 21.8 14.7 26.3 25.2 B27 RHK FYL (WMI) 28.4 6.1 13.3 13.9 35.3 23.4 B62 QL (IVMP) FWY (MIV) 12.6 4.8 36.5 25.4 11.1 18.1 B58 ATS FWY (LIV) 10.0 25.1 1.6 9.0 5.9 10.3

TABLE IV (G) Calculated population coverage afforded by different HLA-supertype combinations Phenotypic frequency HLA-supertypes Caucasian N.A Blacks Japanese Chinese Hispanic Average A2, A3 and B7 83.0 86.1  87.5 88.4 86.3 86.2 A2, A3, B7, A24, B44 99.5 98.1 100.0 99.5 99.4 99.3 and A1 99.9 99.6 100.0 99.8 99.9 99.8 A2, A3, B7, A24, B44, A1, B27, B62, and B 58 Motifs indicate the residues defining supertype specificites. The motifs incorporate residues determined on the basis of published data to be recognized by multiple alleles within the supertype. Residues within brackets are additional residues also predicted to be tolerated by multiple alleles within the supertype.

TABLE V Frequently Occurring Motifs avrg. % Name identity Description Potential Function zf-C2H2 34% Zinc finger, C2H2 type Nucleic acid-binding protein functions as transcription factor, nuclear location probable cytochrome_b_N 68% Cytochrome b(N- membrane bound oxidase, generate terminal)/b6/petB superoxide Ig 19% Immunoglobulin domain domains are one hundred amino acids long and include a conserved intradomain disulfide bond. WD40 18% WD domain, G-beta repeat tandem repeats of about 40 residues, each containing a Trp-Asp motif. Function in signal transduction and protein interaction PDZ 23% PDZ domain may function in targeting signaling molecules to sub-membranous sites LRR 28% Leucine Rich Repeat short sequence motifs involved in protein—protein interactions Pkinase 23% Protein kinase domain conserved catalytic core common to both serine/threonine and tyrosine protein kinases containing an ATP binding site and a catalytic site PH 16% PH domain pleckstrin homology involved in intracellular signaling or as constituents of the cytoskeleton EGF 34% EGF-like domain 30–40 amino-acid long found in the extracellular domain of membrane- bound proteins or in secreted proteins Rvt 49% Reverse transcriptase (RNA-dependent DNA polymerase) Ank 25% Ank repeat Cytoplasmic protein, associates integral membrane proteins to the cytoskeleton Oxidored_q1 32% NADH- membrane associated. Involved in Ubiquinone/plastoquinone proton translocation across the (complex I), various chains membrane Efhand 24% EF hand calcium-binding domain, consists of a12 residue loop flanked on both sides by a 12 residue alpha-helical domain Rvp 79% Retroviral aspartyl Aspartyl or acid proteases, centered on protease a catalytic aspartyl residue Collagen 42% Collagen triple helix repeat extracellular structural proteins involved (20 copies) in formation of connective tissue. The sequence consists of the G-X-Y and the polypeptide chains forms a triple helix. Fn3 20% Fibronectin type III domain Located in the extracellular ligand- binding region of receptors and is about 200 amino acid residues long with two pairs of cysteines involved in disulfide bonds 7tm_1 19% 7 transmembrane receptor seven hydrophobic transmembrane (rhodopsin family) regions, with the N-terminus located extracellularly while the C-terminus is cytoplasmic. Signal through G proteins

TABLE VI Motifs and Post-translational Modifications of 161P2F10B N-glycosylation site: Number of matches: 10 1 236–239 NFSL (SEQ ID NO: 41) 2 279–282 NGSF (SEQ ID NO: 42) 3 290–293 NGSV (SEQ ID NO: 43) 4 426–429 NLSC (SEQ ID NO: 44) 5 533–536 NGTH (SEQ ID NO: 45) 6 582–585 NSTQ (SEQ ID NO: 46) 7 594–597 NLTQ (SEQ ID NO: 47) 8 687–690 NITH (SEQ ID NO: 48) 9 699–702 NRTS (SEQ ID NO: 49) 10 789–792 NKSH (SEQ ID NO: 50) cAMP- and cGMP-dependent protein kinase phosphorylation site 14–17 KKNT (SEQ ID NO: 51) Protein kinase C phosphorylation site Number of matches: 13 1 17–19 TLK 2 53–55 SCR 3 428–430 SCR 4 62–64 SFR 5 92–94 STR 6 240–242 SSK 7 335–337 SAR 8 53–55 SCR 9 428–430 SCR 10 502–504 SFK 11 603–605 TVK 12 676–678 SQK 13 698–700 SNR Casein kinase II phosphorylation site Number of matches: 15 1 88–91 TCVE (SEQ ID NO: 52) 2 106–109 TRLE (SEQ ID NO: 53) 3 114–117 SCSD (SEQ ID NO: 54) 4 138–141 SWLE (SEQ ID NO: 55) 5 240–243 SSKE (SEQ ID NO: 56) 6 502–505 SFKE (SEQ ID NO: 57) 7 507–510 TEVE (SEQ ID NO: 58) 8 551–554 SHAE (SEQ ID NO: 59) 9 584–587 TQLE (SEQ ID NO: 60) 10 596–599 TQEE (SEQ ID NO: 61) 11 660–663 TVPD (SEQ ID NO: 62) 12 704–707 SQYD (SEQ ID NO: 63) 13 813–816 TNVE (SEQ ID NO: 64) 14 817–820 SCPE (SEQ ID NO: 65) 15 846–849 TGLD (SEQ ID NO: 66) Tyrosine kinase phosphorylation site 700–706 RTSDSQY (SEQ ID NO: 67) N-myristoylation site Number of matches: 11 1 38–43 GLGLGL (SEQ ID NO: 68) 2 40–45 GLGLGL (SEQ ID NO: 69) 3 38–43 GLGLGL (SEQ ID NO: 70) 4 40–45 GLGLGL (SEQ ID NO: 71) 5 65–70 GLENCR (SEQ ID NO: 72) 6 222–227 GIIDNN (SEQ ID NO: 73) 7 263–268 GLKAAT (SEQ ID NO: 74) 8 273–278 GSEVAI (SEQ ID NO: 75) 9 280–285 GSFPSI (SEQ ID NO. 76) 10 331–336 GGPVSA (SEQ ID NO: 77) 11 374–379 GMDQTY (SEQ ID NO: 78) Cell attachment sequence 78–80 RGD Somatomedin B domain signature Number of matches: 2 1 69–89 CRCDVACKDRGDCCWDFEDTC (SEQ ID NO: 79) 2 113–133 CSCSDDCLQKKDCCADYKSVC (SEQ ID NO: 80)

TABLE VII Search Peptides 161P2F10B variant 1 (SEQ ID NO: 81)   1 MESTLTLATE QPVKKNTLKK YKIACIVLLA LLVIMSLGLG LGLGLRKLEK QGSCRKKCFD  61 ASFRGLENCR CDVACKDRGD CCWDFEDTCV ESTRIWMCNK FRCGETRLEA SLCSCSDDCL 121 QKKDCCADYK SVCQGETSWL EENCDTAQQS QCPEGFDLPP VILFSMDGFR AEYLYTWDTL 181 MPNINKLKTC GIHSKYMRAM YPTKTFPNHY TIVTGLYPES HGIIDNNMYD VNLNKNFSLS 241 SKEQNNPAWW HGQPMWLTAM YQGLKAATYF WPGSEVAING SFPSIYMPYN GSVPFEERIS 301 TLLKWLDLPK AERPRFYTMY FEEPDSSGHA GGPVSARVIK ALQVVDHAFG MLMEGLKQRN 361 LHNCVNIILL ADHGMDQTYC NKMEYMTDYF PRINFFYMYE GPAPRIRAHN IPHDFFSFNS 421 EEIVRNLSCR KPDQHFKPYL TPDLPKRLHY AKNVRIDKVH LFVDQQWLAV RSKSNTNCGG 481 GNHGYNNEFR SMEAIFLAHG PSFKEKTEVE PFENIEVYNL MCDLLRIQPA PNNGTHGSLN 541 HLLKVPFYEP SHAEEVSKFS VCGFANPLPT ESLDCFCPHL QNSTQLEQVN QMLNLTQEEI 601 TATVKVNLPF GRPRVLQKNV DHCLLYHREY VSGFGKAMRM PMWSSYTVPQ LGDTSPLPPT 661 VPDCLRADVR VPPSESQKCS FYLADKNITH GFLYPPASNR TSDSQYDALI TSNLVPMYEE 721 FRKMWDYFHS VLLIKHATER NGVNVVSGPI FDYNYDGHFD APDEITKHLA NTDVPIPTHY 781 FVVLTSCKNK SHTPENCPGW LDVLPFIIPH RPTNVESCPE GKPEALWVEE RFTAHIARVR 841 DVELLTGLDF YQDKVQPVSE ILQLKTYLPT FETTI Variant 2 9-mers

10-mers

15-mers

Variant 3 9-mers PTNVESCPGGKPEALWV (SEQ ID NO: 85) 10-mers RPTNVESCPGGKPEALWVE (SEQ ID NO: 86) 15-mers FIIPHRPTNVESCPGGKPEALWVEERFTA (SEQ ID NO: 87) Variant 4 9-mers TYLPTFETPI (SEQ ID NO: 88) 10-mers KTYLPTFETPI (SEQ ID NO: 89) 15-mers EILQLKTYLPTFETPI (SEQ ID NO: 90)

TABLE VIII Start Subsequence Score V1-HLA-A1-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 3; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 105 SMDGFRAEY 25.000 754 NVESCPEGK 18.000 55 CSDDCLQKK 15.000 446 KTEVEPFEN 11.250 245 WLDLPKAER 10.000 798 VSEILQLKT 6.750 317 QTYCNKMEY 6.250 371 KPDQHFKPY 6.250 10 RCDVACKDR 5.000 314 GMDQTYCNK 5.000 322 KMEYMTDYF 4.500 454 NIEVYNLMC 4.500 29 CVESTRIWM 4.500 650 ITSNLVPMY 2.500 118 DTLMPNINK 2.500 685 VVSGPIFDY 2.500 559 NVDHCLLYH 2.500 711 NTDVPIPTH 2.500 740 WLDVLPFII 2.500 402 FVDQQWLAV 2.500 431 SMEAIFLAH 2.250 610 RVPPSESQK 2.000 379 YLTPDLPKR 2.000 613 PSESQKCSF 1.350 213 GSEVAINGS 1.350 359 NSEEIVRNL 1.350 128 KTCGIHSKY 1.250 326 MTDYFPRIN 1.250 426 NNEFRSMEA 1.125 632 FLYPPASNR 1.000 163 IIDNNMYDV 1.000 512 SLDCFCPHL 1.000 66 CADYKSVCQ 1.000 653 NLVPMYEEF 1.000 606 RADVRVPPS 1.000 54 SCSDDCLQK 1.000 767 WVEERFTAH 0.900 448 EVEPFENIE 0.900 525 QLEQVNQML 0.900 79 WLEENCDTA 0.900 492 HAEEVSKFS 0.900 537 QEEITATVK 0.900 5 GLENCRCDV 0.900 47 RLEASLCSC 0.900 641 TSDSQYDAL 0.750 626 KNITHGFLY 0.625 558 KNVDHCLLY 0.625 783 ELLTGLDFY 0.500 62 KKDCCADYK 0.500 310 LADHGMDQT 0.500 167 NMYDVNLNK 0.500 562 HCLLYHREY 0.500 197 LTAMYQGLK 0.500 699 FDAPDEITK 0.500 787 GLDFYQDKV 0.500 83 NCDTAQQSQ 0.500 593 DTSPLPPTV 0.500 284 VVDHAFGML 0.500 144 KTFPNHYTI 0.500 417 NCGGGNHGY 0.500 350 NIPHDFFSF 0.500 97 DLPPVILFS 0.500 742 DVLPFIIPH 0.500 250 KAERPRFYT 0.450 292 LMEGLKQRN 0.450 677 ATERNGVNV 0.450 261 FEEPDSSGH 0.450 618 KCSFYLADK 0.400 571 VSGFGKAMR 0.300 536 TQEEITATV 0.270 193 QPMWLTAMY 0.250 687 SGPIFDYNY 0.250 772 FTAHIARVR 0.250 655 VPMYEEFRK 0.250 476 HGSLNHLLK 0.250 712 TDVPIPTHY 0.250 550 FGRPRVLQK 0.250 601 VPDCLRADV 0.250 578 MRMPMWSSY 0.250 546 VNLPFGRPR 0.250 461 MCDLLRIQP 0.250 395 RIDKVHLFV 0.250 586 YTVPQLGDT 0.250 96 FDLPPVILF 0.250 509 PTESLDCFC 0.225 758 CPEGKPEAL 0.225 733 TPENCPGWL 0.225 493 AEEVSKFSV 0.225 43 CGETRLEAS 0.225 722 VVLTSCKNK 0.200 746 FIIPHRPTN 0.200 436 FLAHGPSFK 0.200 743 VLPFIIPHR 0.200 133 HSKYMRAMY 0.150 201 YQGLKAATY 0.150 231 GSVPFEERI 0.150 686 VSGPIFDYN 0.150 382 PDLPKRLHY 0.125 191 HGQPMWLTA 0.125 701 APDEITKHL 0.125 V2-HLA-A1-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 5; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 2 CSDDCLQRK 15.000 9 RKDGCADYK 0.500 1 SCSDDCLQR 0.500 5 DCLQRKDCC 0.010 8 QRKDCCADY 0.005 3 SDDCLQRKD 0.003 6 CLQRKDCCA 0.001 4 DDCLQRKDC 0.001 7 LQRKDCCAD 0.000 V3-HLA-A1-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 7; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 3 NVESCPGGK 18 6 SCPGGKPEA 0.02 5 ESCPGGKPE 0.015 9 GGKPEALWV 0.013 2 TNVESCPGG 0.005 7 CPGGKPEAL 0.003 1 PTNVESCPG 0.003 4 VESCPGGKP 0 8 PGGKPEALW 0 V4-HLA-A1-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 9; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 2 YLPTFETPI 0.01 1 TYLPTFETP 0.001

TABLE IX Start Subsequence Score V1-HLA-A1-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 3; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 798 VSEILQLKTY 67.500 711 NTDVPIPTHY 62.500 326 MTDYFPRINF 62.500 781 DVELLTGLDF 45.000 448 EVEPFENIEV 45.000 220 GSFPSIYMPY 37.500 381 TPDLPKRLHY 31.250 310 LADHGMDQTY 25.000 686 VSGPIFDYNY 15.000 213 GSEVAINGSF 13.500 402 FVDQQWLAVR 10.000 559 NVDHCLLYHR 10.000 613 PSESQKCSFY 6.750 525 QLEQVNQMLN 4.500 567 HREYVSGFGK 4.500 492 HAEEVSKFSV 4.500 536 TQEEITATVK 2.700 684 NVVSGPIFDY 2.500 698 HFDAPDEITK 2.500 284 VVDHAFGMLM 2.500 658 YEEFRKMWDY 2.250 446 KTEVEPFENI 2.250 762 KPEALWVEER 2.250 742 DVLPFIIPHR 2.000 119 TLMPNINKLK 2.000 767 WVEERFTAHI 1.800 53 CSCSDDCLQK 1.500 641 TSDSQYDALI 1.500 104 FSMDGFRAEY 1.500 359 NSEEIVRNLS 1.350 349 HNIPHDFFSF 1.250 328 DYFPRINFFY 1.250 601 VPDCLRADVR 1.250 95 GFDLPPVILF 1.250 157 YPESHGIIDN 1.125 654 LVPMYEEFRK 1.000 653 NLVPMYEEFR 1.000 649 LITSNLVPMY 1.000 47 RLEASLCSCS 0.900 29 CVESTRIWMC 0.900 5 GLENCRCDVA 0.900 110 RAEYLYTWDT 0.900 79 WLEENCDTAQ 0.900 431 SMEAIFLAHG 0.900 356 FSFNSEEIVR 0.750 785 LTGLDFYQDK 0.500 623 LADKNITHGF 0.500 83 NCDTAQQSQC 0.500 66 CADYKSVCQG 0.500 541 TATVKVNLPF 0.500 10 RCDVACKDRG 0.500 794 KVQPVSEILQ 0.500 787 GLDFYQDKVQ 0.500 163 IIDNNMYDVN 0.500 512 SLDCFCPHLQ 0.500 461 MCDLLRIQPA 0.500 217 AINGSFPSIY 0.500 97 DLPPVILFSM 0.500 292 LMEGLKQRNL 0.450 487 FYEPSHAEEV 0.450 92 CPEGFDLPPV 0.450 43 CGETRLEASL 0.450 235 FEERISTLLK 0.450 454 NIEVYNLMCD 0.450 261 FEEPDSSGHA 0.450 758 CPEGKPEALW 0.450 338 MYEGPAPRIR 0.450 316 DQTYCNKMEY 0.375 756 ESCPEGKPEA 0.300 263 EPDSSGHAGG 0.250 740 WLDVLPFIIP 0.250 586 YTVPQLGDTS 0.250 314 GMDQTYCNKM 0.250 479 LNHLLKVPFY 0.250 139 AMYPTKTFPN 0.250 168 MYDVNLNKNF 0.250 25 FEDTCVESTR 0.250 377 KPYLTPDLPK 0.250 105 SMDGFRAEYL 0.250 591 LGDTSPLPPT 0.250 166 NNMYDVNLNK 0.250 144 KTFPNHYTIV 0.250 371 KPDQHFKPYL 0.250 690 IFDYNYDGHF 0.250 426 NNEFRSMEAI 0.225 74 QGETSWLEEN 0.225 360 SEEIVRNLSC 0.225 677 ATERNGVNVV 0.225 570 YVSGFGKAMR 0.200 129 TCGIHSKYMR 0.200 721 FVVLTSCKNK 0.200 682 GVNVVSGPIF 0.200 196 WLTAMYQGLK 0.200 434 AIFLAHGPSF 0.200 54 SCSDDCLQKK 0.200 478 SLNHLLKVPF 0.200 437 LAHGPSFKEK 0.200 250 KAERPRFYTM 0.180 231 GSVPFEERIS 0.150 192 GQPMWLTAMY 0.150 V2-HLA-A1-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 5; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 1 CSCSDDCLQR 0.750 2 SCSDDCLQRK 0.200 3 CSDDCLQRKD 0.075 10 RKDCCADYKS 0.050 4 SDDCLQRKDC 0.025 6 DCLQRKDCCA 0.010 8 LQRKDCCADY 0.002 9 QRKDCCADYK 0.001 5 DDCLQRKDCC 0.001 7 CLQRKDCCAD 0.000 V3-HLA-A1-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 7; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 6 ESCPGGKPEA 0.3 4 NVESCPGGKP 0.09 3 TNVESCPGGK 0.05 7 SCPGGKPEAL 0.01 2 PTNVESCPGG 0.005 8 CPGGKPEALW 0.005 1 RPTNVESCPG 0.003 10 GGKPEALWVE 0 9 PGGKPEALWV 0 5 VESCPGGKPE 0 V4-HLA-A1-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 9; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 2 TYLPTFETPI 0.005 1 KTYLPTFETP 0.003

TABLE X Start Subsequence Score V1-HLA-A0201-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 3; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 663 KMWDYFHSV 11367.476 563 CLLYHREYV 693.538 325 YMTDYFPRI 270.002 807 YLPTFETTI 182.365 119 TLMPNINKL 181.794 196 WLTAMYQGL 147.401 459 NLMCDLLRI 88.783 113 YLYTWDTLM 73.129 547 NLPFGRPRV 69.552 765 ALWVEERFT 68.037 740 WLDVLPFII 45.649 238 RISTLLKWL 37.157 155 GLYPESHGI 33.385 512 SLDCFCPHL 32.471 579 RMPMWSSYT 29.601 199 AMYQGLKAA 26.408 395 RIDKVHLFV 21.039 402 FVDQQWLAV 19.036 524 TQLEQVNQM 17.575 747 IIPHRPTNV 16.258 163 IIDNNMYDV 14.957 400 HLFVDQQWL 14.781 787 GLDFYQDKV 13.632 90 SQCPEGFDL 12.562 693 YNYDGHFDA 11.352 283 QVVDHAFGM 10.337 300 NLHNCVNII 9.838 555 VLQKNVDHC 9.518 532 MLNLTQEEI 8.691 570 YVSGFGKAM 7.599 802 LQLKTYLPT 7.129 500 SVCGFANPL 7.103 805 KTYLPTFET 6.723 430 RSMEAIFLA 6.563 277 RVIKALQVV 5.739 171 VNLNKNFSL 5.087 59 CLQKKDCCA 4.968 534 NLTQEEITA 4.968 383 DLPKRLHYA 4.713 800 EILQLKTYL 4.483 5 GLENCRCDV 4.451 452 FENIEVYNL 4.395 307 IILLADHGM 4.297 714 VPIPTHYFV 4.245 477 GSLNHLLKV 3.864 111 AEYLYTWDT 3.478 488 YEPSHAEEV 3.048 79 WLEENCDTA 2.938 580 MPMWSSYTV 2.856 30 VESTRIWMC 2.833 217 AINGSFPSI 2.726 649 LITSNLVPM 2.671 51 SLCSCSDDC 2.434 670 SVLLIKHAT 2.413 449 VEPFENIEV 2.299 380 LTPDLPKRL 2.068 21 CCWDFEDTC 2.055 144 KTFPNHYTI 1.876 297 KQRNLHNCV 1.876 240 STLLKWLDL 1.866 536 TQEEITATV 1.850 535 LTQEEITAT 1.659 356 FSFNSEEIV 1.552 528 QVNQMLNLT 1.500 583 WSSYTVPQL 1.475 622 YLADKNITH 1.405 525 QLEQVNQML 1.367 794 KVQPVSEIL 1.314 72 VCQGETSWL 1.304 467 IQPAPNNGT 1.284 233 VPFEERIST 1.255 192 GQPMWLTAM 1.159 456 EVYNLMCDL 1.032 131 GIHSKYMRA 1.025 280 KALQVVDHA 1.007 291 MLMEGLKQR 0.884 427 NEFRSMEAI 0.846 784 LLTGLDFYQ 0.808 447 TEVEPFENI 0.774 715 PIPTHYFVV 0.750 250 KAERPRFYT 0.740 98 LPPVILFSM 0.735 47 RLEASLCSC 0.731 330 FPRINFFYM 0.687 474 GTHGSLNHL 0.682 337 YMYEGPAPR 0.650 274 VSARVIKAL 0.545 521 QNSTQLEQV 0.512 540 ITATVKVNL 0.504 493 AEEVSKFSV 0.502 270 AGGPVSARV 0.454 665 WDYFHSVLL 0.437 790 FYQDKVQPV 0.419 44 GETRLEASL 0.415 190 WHGQPMWLT 0.411 656 PMYEEFRKM 0.394 436 FLAHGPSFK 0.377 527 EQVNQMLNL 0.374 115 YTWDTLMPN 0.373 708 HLANTDVPI 0.355 V2-A0201-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 5; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 6 CLQRKDCCA 4.968 5 DCLQRKDCC 0.004 4 DDCLQRKDC 0.001 1 SCSDDCLQR 0.000 2 CSDDCLQRK 0.000 7 LQRKDCCAD 0.000 9 RKDCCADYK 0.000 3 SDDCLQRKD 0.000 8 QRKDCCADY 0.000 V3-HLA-A2-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 7; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 9 GGKPEALWV 0.087 7 CPGGKPEAL 0.068 6 SCPGGKPEA 0.032 2 TNVESCPGG 0.002 4 VESCPGGKP 0 1 PTNVESCPG 0 3 NVESCPGGK 0 8 PGGKPEALW 0 5 ESCPGGKPE 0 V4-HLA-A2-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 9; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 2 YLPTFETPI 182.365 1 TYLPTFETP 0

TABLE XI Start Subsequence Score V1-HLA-A0201-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 3; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 663 KMWDYFHSVL 2862.980 337 YMYEGPAPRI 454.740 765 ALWVEERFTA 239.160 102 ILFSMDGFRA 181.243 632 FLYPPASNRT 109.693 379 YLTPDLPKRL 98.267 162 GIIDNNMYDV 90.183 309 LLADHGMDQT 58.537 115 YTWDTLMPNI 52.169 579 RMPMWSSYTV 50.232 746 FIIPHRPTNV 43.992 555 VLQKNVDHCL 36.316 407 WLAVRSKSNT 34.279 34 RIWMCNKFRC 32.884 524 TQLEQVNQML 32.857 600 TVPDCLRADV 24.952 801 ILQLKTYLPT 19.003 199 AMYQGLKAAT 17.222 534 NLTQEEITAT 17.140 105 SMDGFRAEYL 16.632 21 CCWDFEDTCV 15.450 531 QMLNLTQEEI 13.661 520 LQNSTQLEQV 13.511 614 SESQKCSFYL 13.251 648 ALITSNLVPM 11.426 51 SLCSCSDDCL 10.468 387 RLHYAKNVRI 10.433 71 SVCQGETSWL 10.281 120 LMPNINKLKT 9.149 300 NLHNCVNIIL 8.759 795 VQPVSEILQL 8.469 233 VPFEERISTL 8.271 144 KTFPNHYTIV 7.693 4 RGLENCRCDV 6.887 535 LTQEEITATV 6.733 97 DLPPVILFSM 4.970 282 LQVVDHAFGM 4.966 400 HLFVDQQWLA 4.687 767 WVEERFTAHI 4.187 371 KPDQHFKPYL 4.080 224 SIYMPYNGSV 3.978 786 TGLDFYQDKV 3.375 622 YLADKNITHG 3.233 207 ATYFWPGSEV 3.091 546 VNLPFGRPRV 2.856 714 VPIPTHYFVV 2.753 458 YNLMCDLLRI 2.666 532 MLNLTQEEIT 2.545 713 DVPIPTHYFV 2.510 499 FSVCGFANPL 2.438 799 SEILQLKTYL 2.285 291 MLMEGLKQRN 1.922 283 QVVDHAFGML 1.893 136 YMRAMYPTKT 1.882 554 RVLQKNVDHC 1.813 155 GLYPESHGII 1.779 547 NLPFGRPRVL 1.752 455 IEVYNLMCDL 1.624 526 LEQVNQMLNL 1.624 167 NMYDVNLNKN 1.624 484 KVPFYEPSHA 1.521 314 GMDQTYCNKM 1.435 123 NINKLKTCGI 1.435 317 QTYCNKMEYM 1.369 128 KTCGIHSKYM 1.328 508 LPTESLDCFC 1.243 358 FNSEEIVRNL 1.210 284 VVDHAFGMLM 1.123 111 AEYLYTWDTL 1.107 805 KTYLPTFETT 1.079 466 RIQPAPNNGT 1.025 139 AMYPTKTFPN 0.999 329 YFPRINFFYM 0.962 640 RTSDSQYDAL 0.894 170 DVNLNKNFSL 0.813 89 QSQCPEGFDL 0.809 28 TCVESTRIWM 0.731 716 IPTHYFVVLT 0.723 306 NIILLADHGM 0.683 242 LLKWLDLPKA 0.680 662 RKMWDYFHSV 0.679 504 FANPLPTESL 0.669 452 FENIEVYNLM 0.667 232 SVPFEERIST 0.652 425 YNNEFRSMEA 0.612 564 LLYHREYVSG 0.608 511 ESLDCFCPHL 0.603 198 TAMYQGLKAA 0.587 401 LFVDQQWLAV 0.572 399 VHLFVDQQWL 0.513 63 KDCCADYKSV 0.507 665 WDYFHSVLLI 0.491 392 KNVRIDKVHL 0.488 29 CVESTRIWMC 0.480 216 VAINGSFPSI 0.468 440 GPSFKEKTEV 0.454 773 TAHIARVRDV 0.444 339 YEGPAPRIRA 0.444 646 YDALITSNLV 0.444 610 RVPPSESQKC 0.435 V2-A0201-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 5; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 7 CLQRKDCCAD 0.015 6 DCLQRKDCCA 0.009 4 SDDCLQRKDC 0.003 8 LQRKDCCADY 0.001 2 SCSDDCLQRK 0.001 5 DDCLQRKDCC 0.000 1 CSCSDDCLQR 0.000 10 RKDCCADYKS 0.000 3 CSDDCLQRKD 0.000 9 QRKDCCADYK 0.000 V3-HLA-A2-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 7; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 7 SCPGGKPEAL 0.068 9 PGGKPEALWV 0.055 6 ESCPGGKPEA 0.002 5 VESCPGGKPE 0 8 CPGGKPEALW 0 1 RPTNVESCPG 0 3 TNVESCPGGK 0 10 GGKPEALWVE 0 2 PTNVESCPGG 0 4 NVESCPGGKP 0 V4-HLA-A2-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 9; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 2 TYLPTFETPI 0.02 1 KTYLPTFETP 0.002

TABLE XII Start Subsequence Score V1-HLA-A3-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 3; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 167 NMYDVNLNK 300.000 314 GMDQTYCNK 60.000 632 FLYPPASNR 45.000 242 LLKWLDLPK 40.000 337 YMYEGPAPR 30.000 663 KMWDYFHSV 27.000 436 FLAHGPSFK 20.000 136 YMRAMYPTK 20.000 105 SMDGFRAEY 18.000 120 LMPNINKLK 15.000 155 GLYPESHGI 13.500 379 YLTPDLPKR 9.000 803 QLKTYLPTF 9.000 743 VLPFIIPHR 9.000 291 MLMEGLKQR 6.750 245 WLDLPKAER 6.000 322 KMEYMTDYF 6.000 102 ILESMDGER 6.000 672 LLIKHATER 6.000 325 YMTDYFPRI 5.400 653 NLVPMYEEF 4.500 32 STRIWMCNK 4.500 685 VVSGPIFDY 4.050 387 RLHYAKNVR 4.000 610 RVPPSESQK 3.000 400 HLFVDQQWL 3.000 281 ALQVVDHAF 3.000 113 YLYTWDTLM 3.000 459 NLMCDLLRI 2.700 618 KCSFYLADK 2.700 783 ELLTGLDFY 2.700 119 TLMPNINKL 2.025 144 KTFPNHYTI 2.025 317 QTYCNKMEY 2.000 754 NVESCPEGK 2.000 363 IVRNLSCRK 2.000 350 NIPHDFFSF 1.800 431 SMEAIFLAH 1.800 203 GLKAATYFW 1.800 512 SLDCFCPHL 1.800 300 NLHNCVNII 1.800 807 YLPTFETTI 1.800 740 WLDVLPFII 1.800 787 GLDFYQDKV 1.800 722 VVLTSCKNK 1.500 128 KTCGIHSKY 1.350 118 DTLMPNINK 1.350 654 LVPMYEEFR 1.200 34 RIWMCNKFR 1.000 272 GPVSARVIK 0.900 655 VPMYEEFRK 0.900 405 QQWLAVRSK 0.900 197 LTAMYQGLK 0.900 568 REYVSGFGK 0.900 525 QLEQVNQML 0.900 199 AMYQGLKAA 0.750 797 PVSEILQLK 0.675 532 MLNLTQEEI 0.600 5 GLENCRCDV 0.600 8 NCRCDVACK 0.600 564 LLYHREYVS 0.600 555 VLQKNVDHC 0.600 384 LPKRLHYAK 0.600 708 HLANTDVPI 0.600 650 ITSNLVPMY 0.600 196 WLTAMYQGL 0.600 390 YAKNVRIDK 0.600 542 ATVKVNLPF 0.450 101 VILFSMDGF 0.450 794 KVQPVSEIL 0.405 534 NLTQEEITA 0.400 54 SCSDDCLQK 0.400 622 YLADKNITH 0.400 805 KTYLPTFET 0.338 79 WLEENCDTA 0.300 579 RMPMWSSYT 0.300 47 RLEASLCSC 0.300 563 CLLYHREYV 0.300 577 AMRMPMWSS 0.270 362 EIVRNLSCR 0.270 217 AINGSFPSI 0.270 482 LLKVPFYEP 0.270 500 SVCGFANPL 0.270 269 HAGGPVSAR 0.270 126 KLKTCGIHS 0.240 474 GTHGSLNHL 0.203 51 SLCSCSDDC 0.200 258 TMYFEEPDS 0.200 547 NLPFGRPRV 0.200 59 CLQKKDCCA 0.200 550 FGRPRVLQK 0.180 290 GMLMEGLKQ 0.180 484 KVPFYEPSH 0.180 371 KPDQHFKPY 0.180 55 CSDDCLQKK 0.150 139 AMYPTKTFP 0.150 450 EPFENIEVY 0.135 481 HLLKVPFYE 0.135 241 TLLKWLDLP 0.135 456 EVYNLMCDL 0.135 V2-HLA-A3-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 5; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 6 CLQRKDCCA 0.200 2 CSDDCLQRK 0.150 1 SCSDDCLQR 0.080 9 RKDCCADYK 0.020 8 QRKDCCADY 0.004 5 DCLQRKDCC 0.001 7 LQRKDCCAD 0.001 4 DDCLQRKDC 0.000 3 SDDCLQRKD 0.000 V3-HLA-A3-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 7; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 3 NVESCPGGK 0.6 7 CPGGKPEAL 0.009 6 SCPGGKPEA 0.003 9 GGKPEALWV 0.002 1 PTNVESCPG 0 2 TNVESCPGG 0 8 PGGKPEALW 0 4 VESCPGGKP 0 5 ESCPGGKPE 0 V4-HLA-A3-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 9; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 2 YLPTFETPI 1.8 1 TYLPTFETP 0

TABLE XIII Start Subsequence Score V1-HLA-A3-10mers-161P2F10B Each peptide is a portion of SEQ ID NO 3; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 126 KLKTCGIHSK 90.000 241 TLLKWLDLPK 60.000 119 TLMPNINKLK 33.750 663 KMWDYFHSVL 27.000 653 NLVPMYEEFR 27.000 383 DLPKRLHYAK 18.000 196 WLTAMYQGLK 18.000 290 GMLMEGLKQR 13.500 377 KPYLTPDLPK 9.000 337 YMYEGPAPRI 6.750 654 LVPMYEEFRK 6.000 671 VLLIKHATER 6.000 155 GLYPESHGII 4.050 684 NVVSGPIFDY 4.050 577 AMRMPMWSSY 4.000 102 ILFSMDGFRA 3.000 785 LTGLDFYQDK 3.000 765 ALWVEERFTA 3.000 400 HLFVDQQWLA 3.000 478 SLNHLLKVPF 2.000 226 YMPYNGSVPF 2.000 559 NVDHCLLYHR 1.800 314 GMDQTYCNKM 1.800 300 NLHNCVNIIL 1.800 402 FVDQQWLAVR 1.800 217 AINGSFPSIY 1.800 721 FVVLTSCKNK 1.500 220 GSFPSIYMPY 1.350 543 TVKVNLPFGR 1.200 649 LITSNLVPMY 1.200 330 FPRINFFYMY 1.080 762 KPEALWVEER 1.080 434 AIFLAHGPSF 1.000 531 QMLNLTQEEI 0.900 105 SMDGFRAEYL 0.900 295 GLKQRNLHNC 0.900 555 VLQKNVDHCL 0.900 362 EIVRNLSCRK 0.900 536 TQEEITATVK 0.900 632 FLYPPASNRT 0.750 796 QPVSEILQLK 0.675 97 DLPPVILFSM 0.608 742 DVLPFIIPHR 0.608 51 SLCSCSDDCL 0.600 682 GVNVVSGPIF 0.600 579 RMPMWSSYTV 0.600 5 GLENCRCDVA 0.600 387 RLHYAKNVRI 0.600 247 DLPKAERPRF 0.600 570 YVSGFGKAMR 0.600 393 NVRIDKVHLF 0.600 199 AMYQGLKAAT 0.500 139 AMYPTKTFPN 0.450 648 ALITSNLVPM 0.450 379 YLTPDLPKRL 0.450 437 LAHGPSFKEK 0.450 802 LQLKTYLPTF 0.405 162 GIIDNNMYDV 0.405 481 HLLKVPFYEP 0.405 446 KTEVEPFENI 0.405 545 KVNLPFGRPR 0.360 192 GQPMWLTAMY 0.360 34 RIWMCNKFRC 0.300 326 MTDYFPRINF 0.300 711 NTDVPIPTHY 0.300 54 SCSDDCLQKK 0.300 507 PLPTESLDCF 0.300 136 YMRAMYPTKT 0.300 242 LLKWLDLPKA 0.300 686 VSGPIFDYNY 0.270 784 LLTGLDFYQD 0.270 767 WVEERFTAHI 0.270 172 NLNKNFSLSS 0.240 656 PMYEEFRKMW 0.225 115 YTWDTLMPNI 0.225 805 KTYLPTFETT 0.225 144 KTFPNHYTIV 0.225 366 NLSCRKPDQH 0.200 801 ILQLKTYLPT 0.200 356 FSFNSEEIVR 0.200 53 CSCSDDCLQK 0.200 120 LMPNINKLKT 0.200 258 TMYFEEPDSS 0.200 368 SCRKPDQHFK 0.200 113 YLYTWDTLMP 0.200 166 NNMYDVNLNK 0.180 495 EVSKFSVCGF 0.180 740 WLDVLPFIIP 0.180 323 MEYMTDYFPR 0.180 563 CLLYHREYVS 0.180 101 VILFSMDGFR 0.180 203 GLKAATYFWP 0.180 322 KMEYMTDYFP 0.180 534 NLTQEEITAT 0.150 167 NMYDVNLNKN 0.150 309 LLADHGMDQT 0.150 596 PLPPTVPDCL 0.135 280 KALQVVDHAF 0.135 31 ESTRIWMCNK 0.135 474 GTHGSLNHLL 0.135 V2-HLA-A3-10MERS-161P2F10B Each peptide is a portion of SEQ ID NO: 5; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 2 SCSDDCLQRK 0.300 8 LQRKDCCADY 0.120 1 CSCSDDCLQR 0.040 7 CLQRKDCCAD 0.020 9 QRKDCCADYK 0.020 6 DCLQRKDCCA 0.001 10 RKDCCADYKS 0.000 4 SDDCLQRKDC 0.000 5 DDCLQRKDCC 0.000 3 CSDDCLQRKD 0.000 V3-HLA-A3-10MERS-161P2F10B Each peptide is a portion of SEQ ID NO: 7; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 3 TNVESCPGGK 0.027 7 SCPGGKPEAL 0.009 8 CPGGKPEALW 0.005 4 NVESCPGGKP 0.001 6 ESCPGGKPEA 0 10 GGKPEALWVE 0 1 RPTNVESCPG 0 2 PTNVESCPGG 0 9 PGGKPEALWV 0 5 VESCPGGKPE 0 V4-HLA-A3-10MERS-161P2F10B Each peptide is a portion of SEQ ID NO: 9; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 1 KTYLPTFETP 0.045 2 TYLPTFETPI 0.004

TABLE XIV Start Subsequence Score V1-HLA-A11-9MERS-161P2F10B Each peptide is a portion of SEQ ID NO: 3; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 610 RVPPSESQK 6.000 363 IVRNLSCRK 2.000 754 NVESCPEGK 2.000 167 NMYDVNLNK 1.600 722 VVLTSCKNK 1.500 314 GMDQTYCNK 1.200 655 VPMYEEFRK 1.200 568 REYVSGFGK 1.080 32 STRIWMCNK 1.000 197 LTAMYQGLK 1.000 272 GPVSARVIK 0.900 118 DTLMPNINK 0.900 242 LLKWLDLPK 0.800 618 KCSFYLADK 0.600 390 YAKNVRIDK 0.400 654 LVPMYEEFR 0.400 136 YMRAMYPTK 0.400 384 LPKRLHYAK 0.400 436 FLAHGPSFK 0.400 54 SCSDDCLQK 0.400 667 YFHSVLLIK 0.400 720 YFVVLTSCK 0.300 387 RLHYAKNVR 0.240 34 RIWMCNKFR 0.240 797 PVSEILQLK 0.200 8 NCRCDVACK 0.200 120 LMPNINKLK 0.200 632 FLYPPASNR 0.160 337 YMYEGPAPR 0.160 102 ILFSMDGFR 0.160 324 EYMTDYFPR 0.144 405 QQWLAVRSK 0.120 378 PYLTPDLPK 0.120 144 KTFPNHYTI 0.120 672 LLIKHATER 0.120 554 RVLQKNVDH 0.090 283 QVVDHAFGM 0.090 277 RVIKALQVV 0.090 743 VLPFIIPHR 0.080 291 MLMEGLKQR 0.080 357 SFNSEEIVR 0.080 379 YLTPDLPKR 0.080 245 WLDLPKAER 0.080 62 KKDCCADYK 0.060 794 KVQPVSEIL 0.060 537 QEEITATVK 0.060 682 GVNVVSGPI 0.060 484 KVPFYEPSH 0.060 10 RCDVACKDR 0.060 685 VVSGPIFDY 0.060 640 RTSDSQYDA 0.060 2 SFRGLENCR 0.040 476 HGSLNHLLK 0.040 289 FGMLMEGLK 0.040 559 NVDHCLLYH 0.040 317 QTYCNKMEY 0.040 699 FDAPDEITK 0.040 29 CVESTRIWM 0.040 550 FGRPRVLQK 0.040 402 FVDQQWLAV 0.040 269 HAGGPVSAR 0.040 236 EERISTLLK 0.036 362 EIVRNLSCR 0.036 786 TGLDFYQDK 0.030 240 STLLKWLDL 0.030 128 KTCGIHSKY 0.030 474 GTHGSLNHL 0.030 542 ATVKVNLPF 0.030 458 YNLMCDLLR 0.024 663 KMWDYFHSV 0.024 131 GIHSKYMRA 0.024 345 RIRAHNIPH 0.024 155 GLYPESHGI 0.024 203 GLKAATYFW 0.024 395 RIDKVHLFV 0.024 393 NVRIDKVHL 0.020 284 VVDHAFGML 0.020 500 SVCGFANPL 0.020 772 FTAHIARVR 0.020 369 CRKPDQHFK 0.020 71 SVCQGETSW 0.020 55 CSDDCLQKK 0.020 127 LKTCGIHSK 0.020 767 WVEERFTAH 0.020 174 NKNFSLSSK 0.020 544 VKVNLPFGR 0.018 742 DVLPFIIPH 0.018 805 KTYLPTFET 0.018 192 GQPMWLTAM 0.018 90 SQCPEGFDL 0.018 297 KQRNLHNCV 0.018 459 NLMCDLLRI 0.016 130 CGIHSKYMR 0.012 5 GLENCRCDV 0.012 42 RCGETRLEA 0.012 253 RPRFYTMYF 0.012 740 WLDVLPFII 0.012 787 GLDFYQDKV 0.012 616 SQKCSFYLA 0.012 350 NIPHDFFSE 0.012 V2-HLA-A11-9MERS-161P2F10B Each peptide is a portion of SEQ ID NO: 5; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 1 SCSDDCLQR 0.080 9 RKDCCADYK 0.060 2 CSDDCLQRK 0.020 6 CLQRKDCCA 0.004 7 LQRKDCCAD 0.001 8 QRKDCCADY 0.000 5 DCLQRKDCC 0.000 4 DDCLQRKDC 0.000 3 SDDCLQRKD 0.000 V3-HLA-A11-9MERS-161P2F10B Each peptide is a portion of SEQ ID NO: 7; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 3 NVESCPGGK 2 7 CPGGKPEAL 0.002 6 SCPGGKPEA 0.002 9 GGKPEALWV 0.001 1 PTNVESCPG 0 2 TNVESCPGG 0 4 VESCPGGKP 0 8 PGGKPEALW 0 5 ESCPGGKPE 0 V4-HLA-A11-9MERS-161P2F10B Each peptide is a portion of SEQ ID NO: 9; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 2 YLPTFETPI 0.004 1 TYLPTFETP 0.001

TABLE XV Start Subsequence Score V1-HLA-A11-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 3; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 654 LVPMYEEFRK 6.000 377 KPYLTPDLPK 2.400 135 KYMRAMYPTK 2.400 721 FVVLTSCKNK 1.500 543 TVKVNLPFGR 1.200 241 TLLKWLDLPK 1.200 126 KLKTCGIHSK 1.200 785 LTGLDFYQDK 1.000 559 NVDHCLLYHR 0.800 719 HYFVVLTSCK 0.800 389 HYAKNVRIDK 0.800 536 TQEEITATVK 0.600 666 DYFHSVLLIK 0.480 196 WLTAMYQGLK 0.400 402 FVDQQWLAVR 0.400 570 YVSGFGKAMR 0.400 119 TLMPNINKLK 0.400 698 HFDAPDEITK 0.400 435 IFLAHGPSFK 0.300 796 QPVSEILQLK 0.300 383 DLPKRLHYAK 0.240 54 SCSDDCLQKK 0.200 288 AFGMLMEGLK 0.200 368 SCRKPDQHFK 0.200 742 DVLPFIIPHR 0.180 631 GFLYPPASNR 0.180 290 GMLMEGLKQR 0.180 362 EIVRNLSCRK 0.180 336 FYMYEGPAPR 0.160 457 VYNLMCDLLR 0.160 166 NNMYDVNLNK 0.160 671 VLLIKHATER 0.120 235 FEERISTLLK 0.120 545 KVNLPFGRPR 0.120 762 KPEALWVEER 0.120 653 NLVPMYEEFR 0.120 101 VILFSMDGFR 0.120 437 LAHGPSFKEK 0.100 684 NVVSGPIFDY 0.090 129 TCGIHSKYMR 0.080 323 MEYMTDYFPR 0.072 567 HREYVSGFGK 0.060 753 TNVESCPEGK 0.060 271 GGPVSARVIK 0.060 682 GVNVVSGPIF 0.060 489 EPSHAEEVSK 0.060 484 KVPFYEPSHA 0.060 144 KTFPNHYTIV 0.060 398 KVHLFVDQQW 0.060 475 THGSLNHLLK 0.040 117 WDTLMPNINK 0.040 173 LNKNFSLSSK 0.040 313 HGMDQTYCNK 0.040 597 LPPTVPDCLR 0.040 284 VVDHAFGMLM 0.040 53 CSCSDDCLQK 0.040 601 VPDCLRADVR 0.040 549 PFGRPRVLQK 0.040 162 GIIDNNMYDV 0.036 609 VRVPPSESQK 0.030 283 QVVDHAFGML 0.030 640 RTSDSQYDAL 0.030 446 KTEVEPFENI 0.030 474 GTHGSLNHLL 0.030 282 LQVVDHAFGM 0.027 421 GNHGYNNEFR 0.024 663 KMWDYFHSVL 0.024 765 ALWVEERFTA 0.024 579 RMPMWSSYTV 0.024 155 GLYPESHGII 0.024 102 ILFSMDGFRA 0.024 152 IVTGLYPESH 0.020 71 SVCQGETSWL 0.020 304 CVNIILLADH 0.020 207 ATYFWPGSEV 0.020 767 WVEERFTAHI 0.020 197 LTAMYQGLKA 0.020 115 YTWDTLMPNI 0.020 617 QKCSFYLADK 0.020 326 MTDYFPRINF 0.020 317 QTYCNKMEYM 0.020 61 QKKDCCADYK 0.020 393 NVRIDKVHLF 0.020 386 KRLHYAKNVR 0.018 244 KWLDLPKAER 0.018 192 GQPMWLTAMY 0.018 272 GPVSARVIKA 0.018 170 DVNLNKNFSL 0.018 404 DQQWLAVRSK 0.018 400 HLFVDQQWLA 0.016 356 FSFNSEEIVR 0.016 128 KTCGIHSKYM 0.015 378 PYLTPDLPKR 0.012 771 RFTAHIARVR 0.012 268 GHAGGPVSAR 0.012 250 KAERPRFYTM 0.012 108 GFRAEYLYTW 0.012 573 GFGKAMRMPM 0.012 387 RLHYAKNVRI 0.012 V2-HLA-A-11-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 5; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 2 SCSDDCLQRK 0.200 9 QRKDCCADYK 0.020 1 CSCSDDCLQR 0.008 8 LQRKDCCADY 0.006 6 DCLQRKDCCA 0.001 7 CLQRKDCCAD 0.000 10 RKDCCADYKS 0.000 4 SDDCLQRKDC 0.000 5 DDCLQRKDCC 0.000 3 CSDDCLQRKD 0.000 V3-HLA-A11-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 7; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 3 TNVESCPGGK 0.06 8 CPGGKPEALW 0.002 7 SCPGGKPEAL 0.002 4 NVESCPGGKP 0.002 1 RPTNVESCPG 0.001 10 GGKPEALWVE 0 2 PTNVESCPGG 0 6 ESCPGGKPEA 0 9 PGGKPEALWV 0 5 VESCPGGKPE 0 V4-HLA-A11-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 9; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 2 TYLPTFETPI 0.006 1 KTYLPTFETP 0.006

TABLE XVI Start Subsequence Score V1-HLA-A24-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 3, each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 112 EYLYTWDTL 300.000 457 VYNLMCDLL 300.000 328 DYFPRINFF 144.000 156 LYPESHGII 90.000 338 MYEGPAPRI 75.000 666 DYFHSVLLI 50.000 424 GYNNEFRSM 45.000 40 KFRCGETRL 40.000 318 TYCNKMEYM 25.000 288 AFGMLMEGL 24.000 794 KVQPVSEIL 20.160 95 GFDLPPVIL 20.000 435 IFLAHOPSF 15.000 135 KYMRAMYPT 15.000 633 LYPPASNRT 10.800 790 FYQDKVQPV 10.800 806 TYLPTFETT 10.800 359 NSEEIVRNL 10.080 525 QLEQVNQML 10.080 660 EFRKMWDYF 10.000 428 EFRSMEAIF 10.000 569 EYVSGFGKA 9.900 238 RISTLLKWL 9.600 119 TLMPNINKL 9.504 657 MYEEFRKMW 9.000 621 FYLADKNIT 9.000 225 IYMPYNGSV 9.000 200 MYQGLKAAT 9.000 380 LTPDLPKRL 8.640 597 LPPTVPDCL 8.400 140 MYPTKTFPN 7.500 800 EILQLKTYL 7.200 149 HYTIVTGLY 7.000 719 HYFVVLTSC 7.000 701 APDEITKHL 6.720 168 MYDVNLNKN 6.600 736 NCPGWLDVL 6.000 259 MYFEEPDSS 6.000 138 RAMYPTKTF 6.000 758 CPEGKPEAL 6.000 733 TPENCPGWL 6.000 527 EQVNQMLNL 6.000 240 STLLKWLDL 6.000 615 ESQKCSFYL 6.000 165 DNNMYDVNL 6.000 72 VCQGETSWL 6.000 322 KMEYMTDYF 6.000 645 QYDALITSN 6.000 796 QPVSEILQL 6.000 171 VNLNKNFSL 6.000 505 ANPLPTESL 6.000 556 LQKNVDHCL 5.600 347 RAHNIPHDF 5.600 540 ITATVKVNL 5.600 274 VSARVIKAL 5.600 208 TYFWPGSEV 5.500 355 FFSFNSEEI 5.500 620 SFYLADKNI 5.000 474 GTHGSLNHL 4.800 456 EVYNLMCDL 4.800 716 IPTHYFVVL 4.800 196 WLTAMYQGL 4.800 90 SQCPEGFDL 4.800 500 SVCGFANPL 4.800 400 HLFVDQQWL 4.800 284 VVDHAFGML 4.800 776 IARVRDVEL 4.400 542 ATVKVNLPF 4.200 764 EALWVEERF 4.200 281 ALQVVDHAF 4.200 189 WWHGQPMWL 4.000 512 SLDCFCPHL 4.000 583 WSSYTVPQL 4.000 302 HNCVNIILL 4.000 664 MWDYFHSVL 4.000 548 LPFGRPRVL 4.000 52 LCSCSDDCL 4.000 253 RPRFYTMYF 4.000 641 TSDSQYDAL 4.000 653 NLVPMYEEF 3.960 234 PFEERISTL 3.600 350 NIPHDFFSF 3.600 101 VILFSMDGF 3.000 299 RNLHNCVNI 3.000 713 DVPIPTHYF 3.000 683 VNVVSGPIF 3.000 202 QGLKAATYF 3.000 421 QGLKAATYF 2.640 739 GWLDVLPFI 2.520 144 KTFPNHYTI 2.400 368 SCRKPDQHF 2.400 479 LNHLLKVPF 2.400 508 LPTESLDCF 2.400 682 GVNVVSGPI 2.100 88 QQSQCPEGF 2.000 227 MPYNGSVPF 2.000 496 VSKFSVCGF 2.000 248 LPKAERPRF 2.000 803 QLKTYLPTF 2.000 V2-HLA-A24-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 5; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight 5 DCLQRKDCC 0.150 6 CLQRKDCCA 0.150 2 CSDDCLQRK 0.014 8 QRKDCCADY 0.012 1 SCSDDCLQR 0.012 4 DDCLQRKDC 0.010 7 LQRKDCCAD 0.010 9 RKDCCADYK 0.002 3 SDDCLQRKD 0.001 V3-HLA-A24-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 7; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 7 CPGGKPEAL 4 6 SCPGGKPEA 0.165 9 GGKPEALWV 0.12 2 TNVESCPGG 0.018 3 NVESCPGGK 0.015 5 ESCPGGKPE 0.012 8 PGGKPEALW 0.01 1 PTNVESCPG 0.002 4 VESCPGGKP 0.001 V4-HLA-A24-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 9; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 2 YLPTFETPI 1.5 1 TYLPTFETP 1.08

TABLE XVII V1-HLA-A24-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 3; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. Start Subsequence Score 645 QYDALITSNL 280.000 168 MYDVNLNKNF 120.000 565 LYHREYVSGF 100.000 806 TYLPTFETTI 90.000 324 EYMTDYFPRI 90.000 569 EYVSGFGKAM 37.500 112 EYLYTWDTLM 37.500 375 HFKPYLTPDL 28.800 428 EFRSMEAIFL 20.000 790 FYQDKVQPVS 12.600 524 TQLEQVNQML 12.096 392 KNVRIDKVHL 12.000 700 DAPDEITKHL 10.080 690 IFDYNYDGHF 10.000 95 GFDLPPVILF 10.000 487 FYEPSHAEEV 9.900 663 KMWDYFHSVL 9.600 640 RTSDSQYDAL 9.600 633 LYPPASNRTS 9.000 283 QVVDHAFGML 8.640 328 DYFPRINFFY 8.400 280 KALQVVDHAF 8.400 555 VLQKNVDHCL 8.400 371 KPDQHFKPYL 8.000 118 DTLMPNINKL 7.920 200 MYQGLKAATY 7.500 692 DYNYDGHFDA 7.500 757 SCPEGKPEAL 7.200 504 FANPLPTESL 7.200 511 ESLDCFCPHL 7.200 195 MWLTAMYQGL 7.200 732 HTPENCPGWL 7.200 499 FSVCGFANPL 7.200 43 CGETRLEASL 7.200 358 FNSEEIVRNL 6.720 547 NLPFGRPRVL 6.000 170 DVNLNKNFSL 6.000 795 VQPVSEILQL 6.000 89 QSQCPEGFDL 6.000 470 APNNGTHGSL 6.000 209 YFWPGSEVAI 6.000 588 VPQLGDTSPL 6.000 292 LMEGLKQRNL 6.000 379 YLTPDLPKRL 5.760 300 NLHNCVNIIL 5.600 539 EITATVKVNL 5.600 68 DYKSVCQGET 5.500 354 DFFSFNSEEI 5.500 234 PFEERISTLL 5.040 114 LYTWDTLMPN 5.000 318 TYCNKMEYMT 5.000 208 TYFWPGSEVA 5.000 585 SYTVPQLGDT 5.000 735 ENCPGWLDVL 4.800 287 HAFGMLMEGL 4.800 473 NGTHGSLNHL 4.800 474 GTHGSLNHLL 4.800 233 VPFEERISTL 4.800 94 EGFDLPPVIL 4.800 775 HIARVRDVEL 4.400 349 HNIPHDFFSF 4.320 213 GSEVAINGSF 4.200 51 SLCSCSDDCL 4.000 239 ISTLLKWLDL 4.000 517 CPHLQNSTQL 4.000 582 MWSSYTVPQL 4.000 188 AWWHGQPMWL 4.000 776 IARVRDVELL 4.000 347 RAHNIPHDFF 4.000 105 SMDGFRAEYL 4.000 556 LQKNVDHCLL 4.000 456 EVYNLMCDLL 4.000 664 MWDYFHSVLL 4.000 420 GGNHGYNNEF 3.960 478 SLNHLLKVPF 3.600 299 RNLHNCVNII 3.600 446 KTEVEPFENI 3.600 652 SNLVPMYEEF 3.300 247 DLPKAERPRF 3.000 802 LQLKTYLPTF 3.000 87 AQQSQCPEGF 3.000 226 YMPYNGSVPF 3.000 451 PFENIEVYNL 3.000 682 GVNVVSGPIF 3.000 781 DVELLTGLDF 3.000 623 LADKNITHGF 2.800 541 TATVKVNLPF 2.800 32 STRIWMCNKF 2.640 573 GFGKAMRMPM 2.500 367 LSCRKPDQHF 2.400 739 GWLDVLPFII 2.160 681 NGVNVVSGPI 2.100 434 AIFLAHGPSF 2.000 393 NVRIDKVHLF 2.000 737 CPGWLDVLPF 2.000 495 EVSKFSVCGF 2.000 326 MTDYFPRINF 2.000 201 YQGLKAATYF 2.000 V2-HLA-A24-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 5; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 6 DCLQRKDCCA 0.150 8 LQRKDCCADY 0.100 10 RKDCCADYKS 0.022 3 CSDDCLQRKD 0.016 7 CLQRKDCCAD 0.015 2 SCSDDCLQRK 0.014 4 SDDCLQRKDC 0.010 1 CSCSDDCLQR 0.010 5 DDCLQRKDCC 0.010 9 QRKDCCADYK 0.001 V3-HLA-A11-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 7; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 7 SCPGGKPEAL 6 6 ESCPGGKPEA 0.132 8 CPGGKPEALW 0.1 1 RPTNVESCPG 0.002 3 TNVESCPGGK 0.018 4 NVESCPGGKP 0.017 10 GGKPEALWVE 0.012 9 PGGKPEALWV 0.01 2 PTNVESCPGG 0.002 5 VESCPGGKPE 0.001 V4-HLA-A11-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 9; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 2 TYLPTFETPI 90 1 KTYLPTFETP 0.024

TABLE XVIII Start Subsequence Score V1-HLA-B7-9mers-161P2F10B Each peptide is a portion of SEQ ID NO:3; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 343 APRIRAHNI 240.000 330 FPRINFFYM 200.000 393 NVRIDKVHL 200.000 776 IARVRDVEL 120.000 548 LPFGRPRVL 80.000 716 IPTHYFVVL 80.000 796 QPVSEILQL 80.000 597 LPPTVPDCL 80.000 701 APDEITKHL 72.000 552 RPRVLQKNV 40.000 758 CPEGKPEAL 24.000 733 TPENCPGWL 24.000 500 SVCGFANPL 20.000 456 EVYNLMCDL 20.000 98 LPPVILFSM 20.000 794 KVQPVSEIL 20.000 505 ANPLPTESL 18.000 580 MPMWSSYTV 12.000 119 TLMPNINKL 12.000 284 VVDHAFGML 6.000 283 QVVDHAFGM 5.000 570 YVSGFGKAM 5.000 778 RVRDVELLT 5.000 274 VSARVIKAL 4.000 240 STLLKWLDL 4.000 736 NCPGWLDVL 4.000 90 SQCPEGFDL 4.000 714 VPIPTHYFV 4.000 800 EILQLKTYL 4.000 196 WLTAMYQGL 4.000 540 ITATVKVNL 4.000 238 RISTLLKWL 4.000 253 RPRFYTMYF 4.000 72 VCQGETSWL 4.000 474 GTHGSLNHL 4.000 40 KFRCGETRL 4.000 400 HLFVDQQWL 4.000 615 ESQKCSFYL 4.000 171 VNLNKNFSL 4.000 527 EQVNQMLNL 4.000 165 DNNMYDVNL 4.000 583 WSSYTVPQL 4.000 380 LTPDLPKRL 4.000 556 LQKNVDHCL 4.000 52 LCSCSDDCL 4.000 302 HNCVNIILL 4.000 251 AERPRFYTM 3.000 233 VPFEERIST 3.000 409 AVRSKSNTN 3.000 29 CVESTRIWM 2.250 682 GVNVVSGPI 2.000 485 VPFYEPSHA 2.000 611 VPPSESQKC 2.000 297 KQRNLHNCV 2.000 121 MPNINKLKT 2.000 601 VPDCLRADV 1.800 608 DVRVPPSES 1.500 574 FGKAMRMPM 1.500 219 NGSFPSIYM 1.500 288 AFGMLMEGL 1.200 459 NLMCDLLRI 1.200 525 QLEQVNQML 1.200 512 SLDCFCPHL 1.200 193 QPMWLTAMY 1.200 217 AINGSFPSI 1.200 641 TSDSQYDAL 1.200 777 ARVRDVELL 1.200 359 NSEEIVRNL 1.200 470 APNNGTHGS 1.200 453 ENIEVYNLM 1.000 307 IILLADHGM 1.000 113 YLYTWDTLM 1.000 572 SGFGKAMRM 1.000 524 TQLEQVNQM 1.000 129 TCGIHSKYM 1.000 192 GQPMWLTAM 1.000 649 LITSNLVPM 1.000 45 ETRLEASLC 1.000 277 RVIKALQVV 1.000 198 TAMYQGLKA 0.900 577 AMRMPMWSS 0.900 248 LPKAERPRF 0.600 655 VPMYEEFRK 0.600 647 DALITSNLV 0.600 270 AGGPVSARV 0.600 528 QVNQMLNLT 0.500 363 IVRNLSCRK 0.500 670 SVLLIKHAT 0.500 13 VACKDRGDC 0.450 589 PQLGDTSPL 0.400 708 HLANTDVPI 0.400 299 RNLHNCVNI 0.400 807 YLPTFETTI 0.400 475 THGSLNHLL 0.400 452 FENIEVYNL 0.400 94 EGFDLPPVI 0.400 227 MPYNGSVPF 0.400 471 PNNGTHGSL 0.400 211 WPGSEVAIN 0.400 V2-HLA-B7-9mers-161P2F10B Each peptide is a portion of SEQ ID NO:5; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 5 DCLQRKDCC 0.100 6 CLQRKDCCA 0.100 7 LQRKDCCAD 0.100 4 DDCLQRKDC 0.015 1 SCSDDCLQR 0.010 2 CSDDCLQRK 0.003 8 QRKDCCADY 0.002 3 SDDCLQRKD 0.000 9 RKDCCADYK 0.000 V3-HLA-B7-9mers-161P2F10B Each peptide is a portion of SEQ ID NO:7; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight 7 CPGGKPEAL 80 9 GGKPEALWV 0.2 6 SCPGGKPEA 0.1 3 NVESCPGGK 0.015 5 ESCPGGKPE 0.01 2 TNVESCPGG 0.01 8 PGGKPEALW 0.003 4 VESCPGGKP 0.002 1 PTNVESCPG 0.001 V4-HLA-B7-9mers-161P2F10B Each peptide is a portion of SEQ ID NO:9; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight 2 YLPTFETPI 0.4 1 TYLPTFETP 0.001

TABLE XIX Start Subsequence Score V1-HLA-B7-10mers-161P2F10B Each peptide is a portion of SEQ ID NO:3; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 470 APNNGTHGSL 240.000 776 IARVRDVELL 120.000 588 VPQLGDTSPL 80.000 517 CPHLQNSTQL 80.000 233 VPFEERISTL 80.000 655 VPMYEEFRKM 60.000 371 KPDQHFKPYL 24.000 283 QVVDHAFGML 20.000 186 NPAWWHGQPM 20.000 170 DVNLNKNFSL 20.000 456 EVYNLMCDLL 20.000 71 SVCQGETSWL 20.000 504 FANPLPTESL 18.000 409 AVRSKSNTNC 15.000 287 HAFGMLMEGL 12.000 700 DAPDEITKHL 12.000 94 EGFDLPPVIL 6.000 343 APRIRAHNIP 6.000 275 SARVIKALQV 6.000 300 NLHNCVNIIL 4.000 89 QSQCPEGFDL 4.000 775 HIARVRDVEL 4.000 239 ISTLLKWLDL 4.000 392 KNVRIDKVHL 4.000 440 GPSFKEKTEV 4.000 547 NLPFGRPRVL 4.000 795 VQPVSEILQL 4.000 732 HTPENCPGWL 4.000 473 NGTHGSLNHL 4.000 555 VLQKNVDHCL 4.000 511 ESLDCFCPHL 4.000 51 SLCSCSDDCL 4.000 714 VPIPTHYFVV 4.000 757 SCPEGKPEAL 4.000 330 FPRINFFYMY 4.000 663 KMWDYFHSVL 4.000 640 RTSDSQYDAL 4.000 524 TQLEQVNQML 4.000 428 EFRSMEAIFL 4.000 358 FNSEEIVRNL 4.000 735 ENCPGWLDVL 4.000 118 DTLMPNINKL 4.000 539 EITATVKVNL 4.000 556 LQKNVDHCLL 4.000 474 GTHGSLNHLL 4.000 499 FSVCGFANPL 4.000 379 YLTPDLPKRL 4.000 744 LPFIIPHRPT 3.000 648 ALITSNLVPM 3.000 716 IPTHYFVVLT 2.000 552 RPRVLQKNVD 2.000 595 SPLPPTVPDC 2.000 272 GPVSARVIKA 2.000 273 PVSARVIKAL 2.000 508 LPTESLDCFC 2.000 253 RPRFYTMYFE 2.000 121 MPNINKLKTC 2.000 506 NPLPTESLDC 2.000 701 APDEITKHLA 1.800 600 TVPDCLRADV 1.500 218 INGSFPSIYM 1.500 28 TCVESTRIWM 1.500 284 WDHAFGMLM 1.500 43 CGETRLEASL 1.200 270 AGGPVSARVI 1.200 292 LMEGLKQRNL 1.200 105 SMDGFRAEYL 1.200 624 ADKNITHGFL 1.200 188 AWWHGQPMWL 1.200 216 VAINGSFPSI 1.200 92 CPEGFDLPPV 1.200 111 AEYLYTWDTL 1.200 571 VSGFGKAMRM 1.000 423 HGYNNEFRSM 1.000 713 DVPIPTHYFV 1.000 191 HGQPMWLTAM 1.000 393 NVRIDKVHLF 1.000 159 ESHGIIDNNM 1.000 523 STQLEQVNQM 1.000 282 LQVVDHAFGM 1.000 97 DLPPVILFSM 1.000 136 YMRAMYPTKT 1.000 306 NIILLADHGM 1.000 317 QTYCNKMEYM 1.000 131 GIHSKYMRAM 1.000 128 KTCGIHSKYM 1.000 207 ATYFWPGSEV 0.900 198 TAMYQGLKAA 0.900 250 KAERPRFYTM 0.900 12 DVACKDRGDC 0.750 232 SVPFEERIST 0.750 608 DVRVPPSESQ 0.750 337 YMYEGPAPRI 0.600 676 HATERNGVNV 0.600 390 YAKNVRIDKV 0.600 773 TAHIARVRDV 0.600 193 QPMWLTAMYQ 0.600 767 WVEERFTAHI 0.600 580 MPMWSSYTVP 0.600 269 HAGGPVSARV 0.600 V2-HLA-B7-10mers-161P2F10B Each peptide is a portion of SEQ ID NO:5; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 8 LQRKDCCADY 0.200 6 DCLQRKDCCA 0.100 7 CLQRKDCCAD 0.010 1 CSCSDDCLQR 0.010 5 DDCLQRKDCC 0.010 2 SCSDDCLQRK 0.010 4 SDDCLQRKDC 0.004 3 CSDDCLQRKD 0.003 9 QRKDCCADYK 0.001 10 RKDCCADYKS 0.001 V3-HLA-B7-10mers-161P2F10B Each peptide is a portion of SEQ ID NO:7; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 7 SCPGGKPEAL 4 8 CPGGKPEALW 0.6 1 RPTNVESCPG 0.2 6 ESCPGGKPEA 0.1 4 NVESCPGGKP 0.023 9 PGGKPEALWV 0.02 10 GGKPEALWVE 0.01 3 TNVESCPGGK 0.01 2 PTNVESCPGG 0.001 5 VESCPGGKPE 0.001 V4-HLA-A24-10mers-161P2F10B Each peptide is a portion of SEQ ID NO:9; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 2 TYLPTFETPI 0.04 1 KTYLPTFETP 0.01

TABLE XX Start Subsequence Score V1-HLA-B3501-9mers-161P2F10B Each peptide is a portion of SEQ ID NO:3; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 253 RPRFYTMYF 120.000 330 FPRINFFYM 120.000 248 LPKAERPRF 90.000 450 EPFENIEVY 80.000 98 LPPVILFSM 40.000 508 LPTESLDCF 40.000 193 QPMWLTAMY 40.000 133 HSKYMRAMY 30.000 796 QPVSEILQL 30.000 552 RPRVLQKNV 24.000 371 KPDQHFKPY 24.000 343 APRIRAHNI 24.000 597 LPPTVPDCL 20.000 548 LPFGRPRVL 20.000 716 IPTHYFVVL 20.000 227 MPYNGSVPF 20.000 496 VSKFSVCGF 15.000 701 APDEITKHL 12.000 776 IARVRDVEL 9.000 558 KNVDHCLLY 8.000 733 TPENCPGWL 6.000 758 CPEGKPEAL 6.000 347 RAHNIPHDF 6.000 138 RAMYPTKTF 6.000 638 SNRTSDSQY 6.000 233 VPFEERIST 6.000 574 FGKAMRMPM 6.000 583 WSSYTVPQL 5.000 615 ESQKCSFYL 5.000 274 VSARVIKAL 5.000 393 NVRIDKVHL 4.500 453 ENIEVYNLM 4.000 128 KTCGIHSKY 4.000 580 MPMWSSYTV 4.000 714 VPIPTHYFV 4.000 351 IPHDFFSFN 4.000 626 KNITHGFLY 4.000 283 QVVDHAFGM 4.000 524 TQLEQVNQM 4.000 803 QLKTYLPTF 3.000 611 VPPSESQKC 3.000 368 SCRKPDQHF 3.000 359 NSEEIVRNL 3.000 556 LQKNVDHCL 3.000 764 EALWVEERF 3.000 485 VPFYEPSHA 3.000 161 HGIIDNNMY 3.000 180 SSKEQNNPA 3.000 211 WPGSEVAIN 3.000 238 RISTLLKWL 2.000 222 FPSIYMPYN 2.000 562 HCLLYHREY 2.000 685 VVSGPIFDY 2.000 649 LITSNLVPM 2.000 650 ITSNLVPMY 2.000 146 FPNHYTIVT 2.000 218 INGSFPSIY 2.000 634 YPPASNRTS 2.000 107 DGFRAEYLY 2.000 783 ELLTGLDFY 2.000 570 YVSGFGKAM 2.000 121 MPNINKLKT 2.000 113 YLYTWDTLM 2.000 317 QTYCNKMEY 2.000 231 GSVPFEERI 2.000 417 NCGGGNHGY 2.000 219 NGSFPSIYM 2.000 129 TCGIHSKYM 2.000 201 YQGLKAATY 2.000 307 IILLADHGM 2.000 687 SGPIFDYNY 2.000 192 GQPMWLTAM 2.000 489 EPSHAEEVS 2.000 794 KVQPVSEIL 2.000 470 APNNGTHGS 2.000 572 SGFGKAMRM 2.000 430 RSMEAIFLA 2.000 380 LTPDLPKRL 2.000 641 TSDSQYDAL 1.500 203 GLKAATYFW 1.500 350 NIPHDFFSF 1.500 400 HLFVDQQWL 1.500 90 SQCPEGEDL 1.500 72 VCQGETSWL 1.500 124 INKLKTCGI 1.200 61 QKKDCCADY 1.200 778 RVRDVELLT 1.200 601 VPDCLRADV 1.200 297 KQRNLHNCV 1.200 736 NCPGWLDVL 1.000 732 HTPENCPGW 1.000 196 WLTAMYQGL 1.000 28 TCVESTRIW 1.000 683 VNVVSGPIF 1.000 202 QGLKAATYF 1.000 500 SVCGFANPL 1.000 527 EQVNQMLNL 1.000 88 QQSQCPEGF 1.000 713 DVPIPTHYF 1.000 302 HNCVNIILL 1.000 V2-HLA-B35-9mers-161P2F10B Each peptide is a portion of SEQ ID NO:5; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 8 QRKDCCADY 1.200 5 DCLQRKDCC 0.100 6 CLQRKDCCA 0.100 7 LQRKDCCAD 0.045 1 SCSDDCLQR 0.030 2 CSDDCLQRK 0.030 4 DDCLQRKDC 0.010 9 RKDCCADYK 0.001 3 SDDCLQRKD 0.000 V3-HLA-B35-9mers-161P2F10B Each peptide is a portion of SEQ ID NO:7 each start position is specified, the iength of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 7 CPGGKPEAL 20 9 GGKPEALWV 0.9 6 SCPGGKPEA 0.1 8 PGGKPEALW 0.05 5 ESCPGGKPE 0.05 2 TNVESCPGG 0.02 3 NVESCPGGK 0.003 1 PTNVESCPG 0.002 4 VESCPGGKP 0.001 V4-HLA-B35-9mers-161P2F10B Each peptide is a portion of SEQ ID NO:9; each start position is specified, the length of peptide is 9 amino acids, and the end position for each peptide is the start position plus eight. 2 YLPTFETPI 0.4 1 TYLPTFETP 0.001

TABLE XXI Start Subsequence Score V1-HLA-B35-10mers-161P2F10B Each peptide is a portion of SEQ ID NO:3; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 248 LPKAERPRFY 120.000 330 FPRINFFYMY 120.000 655 VPMYEEFRKM 60.000 233 VPFEERISTL 40.000 141 YPTKTFPNHY 40.000 186 NPAWWHGQPM 40.000 737 CPGWLDVLPF 30.000 588 VPQLGDTSPL 30.000 104 FSMDGFRAEY 20.000 470 APNNGTHGSL 20.000 517 CPHLQNSTQL 20.000 180 SSKEQNNPAW 15.000 776 IARVRDVELL 13.500 371 KPDQHFKPYL 12.000 381 TPDLPKRLHY 12.000 686 VSGPIFDYNY 10.000 220 GSFPSIYMPY 10.000 571 VSGFGKAMRM 10.000 511 ESLDCFCPHL 10.000 159 ESHGIIDNNM 10.000 637 ASNRTSDSQY 10.000 89 QSQCPEGFDL 7.500 280 KALQVVDHAF 6.000 700 DAPDEITKHL 6.000 347 RAHNIPHDFF 6.000 577 AMRMPMWSSY 6.000 320 CNKMEYMTDY 6.000 440 GPSFKEKTEV 6.000 384 LPKRLHYAKN 6.000 60 LQKKDCCADY 6.000 499 FSVCGFANPL 5.000 239 ISTLLKWLDL 5.000 367 LSCRKPDQHF 5.000 70 KSVCQGETSW 5.000 556 LQKNVDHCLL 4.500 612 PPSESQKCSF 4.000 640 RTSDSQYDAL 4.000 351 IPHDFFSFNS 4.000 508 LPTESLDCFC 4.000 663 KMWDYFHSVL 4.000 714 VPIPTHYFVV 4.000 28 TCVESTRIWM 4.000 450 EPEENIEVYN 4.000 128 KTCGIHSKYM 4.000 250 KAERPRFYTM 3.600 287 HAFGMLMEGL 3.000 32 STRIWMCNKF 3.000 393 NVRIDKVHLF 3.000 14 ACKDRGDCCW 3.000 392 KNVRIDKVHL 3.000 758 CPEGKPEALW 3.000 541 TATVKVNLPF 3.000 423 HGYNNEFRSM 3.000 506 NPLPTESLDC 3.000 798 VSEILQLKTY 3.000 504 FANPLPTESL 3.000 97 DLPPVILFSM 2.000 316 DQTYCNKMEY 2.000 595 SPLPPTVPDC 2.000 272 GPVSARVIKA 2.000 648 ALITSNLVPM 2.000 479 LNHLLKVPFY 2.000 283 QVVDHAFGML 2.000 416 TNCGGGNHGY 2.000 131 GIHSKYMRAM 2.000 649 LITSNLVPMY 2.000 684 NVVSGPIFDY 2.000 306 NIILLADHGM 2.000 121 MPNINKLKTC 2.000 358 FNSEEIVRNL 2.000 218 INGSFPSIYM 2.000 192 GQPMWLTAMY 2.000 317 QTYCNKMEYM 2.000 757 SCPEGKPEAL 2.000 611 VPPSESQKCS 2.000 744 LPFIIPHRPT 2.000 217 AINGSFPSIY 2.000 191 HGQPMWLTAM 2.000 341 GPAPRIRAHN 2.000 732 HTPENCPGWL 2.000 282 LQVVDHAFGM 2.000 716 IPTHYFVVLT 2.000 94 EGFDLPPVIL 2.000 523 STQLEQVNQM 2.000 619 CSFYLADKNI 2.000 524 TQLEQVNQML 2.000 748 IPHRPTNVES 2.000 390 YAKNVRIDKV 1.800 310 LADHGMDQTY 1.800 275 SARVIKALQV 1.800 92 CPEGFDLPPV 1.800 71 SVCQGETSWL 1.500 213 GSEVAINGSF 1.500 349 HNIPHDFFSF 1.500 795 VQPVSEILQL 1.500 574 FGKAMRMPMW 1.500 496 VSKFSVCGFA 1.500 247 DLPKAERPRF 1.500 552 RPRVLQKNVD 1.200 676 HATERNGVNV 1.200 V2-HLA-B35-10mers-161P2F10B Each peptide is a portion of SEQ ID NO:5; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 8 LQRKDCCADY 6.000 6 DCLQRKDCCA 0.100 1 CSCSDDCLQR 0.075 3 CSDDCLQRKD 0.030 2 SCSDDCLQRK 0.020 7 CLQRKDCCAD 0.015 5 DDCLQRKDCC 0.010 9 QRKDCCADYK 0.006 10 RKDCCADYKS 0.006 4 SDDCLQRKDC 0.003 V3-B35-10mers-161P2F10B Each peptide is a portion of SEQ ID NO:7; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 8 CPGGKPEALW 10 7 SCPGGKPEAL 1 1 RPTNVESCPG 0.6 6 ESCPGGKPEA 0.5 9 PGGKPEALWV 0.03 10 GGKPEALWVE 0.03 3 TNVESCPGGK 0.02 4 NVESCPGGKP 0.003 2 PTNVESCPGG 0.001 5 VESCPGGKPE 0.001 V4-HLA-B35-10mers-161P2F10B Each peptide is a portion of SEQ ID NO:9; each start position is specified, the length of peptide is 10 amino acids, and the end position for each peptide is the start position plus nine. 2 TYLPTFETPI 0.04 1 KTYLPTFETP 0.02

TABLE XXII Pos 123456789 score V1-HLA-A1-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 81; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 165 SMDGFRAEY 29 431 KPDQHFKPY 28 442 PDLPKRLHY 26 188 KTCGIHSKY 24 618 KNVDHCLLY 23 710 ITSNLVPMY 23 858 VSEILQLKT 23 8 ATEQPVKKN 21 193 HSKYMRAMY 21 202 PTKTFPNHY 21 377 QTYCNKMEY 21 491 SMEAIFLAH 21 209 HYTIVTGLY 19 391 PRINFFYMY 19 462 FVDQQWLAV 19 477 NCGGGNHGY 19 514 NIEVYNLMC 19 638 MRMPMWSSY 19 772 TDVPIPTHY 19 859 SEILQLKTY 19 13 VKKNTLKKY 18 389 YFPRINFFY 18 455 RIDKVHLFV 18 686 KNITHGFLY 18 737 ATERNGVNV 18 745 VVSGPIFDY 18 843 ELLTGLDFY 18 152 CPEGFDLPP 17 167 DGFRAEYLY 17 217 YPESHGIID 17 221 HGIIDNNMY 17 261 YQGLKAATY 17 281 SFPSIYMPY 17 371 ADHGMDQTY 17 420 SEEIVRNLS 17 674 SESQKCSFY 17 698 SNRTSDSQY 17 747 SGPIFDYNY 17 771 NTDVPIPTH 17 839 VRDVELLTG 17 115 CSDDCLQKK 16 134 QGETSWLEE 16 253 QPMWLTAMY 16 312 ERPRFYTMY 16 381 NKMEYMTDY 16 386 MTDYFPRIN 16 506 KTEVEPFEN 16 510 EPFENIEVY 16 540 NHLLKVPFY 16 569 PTESLDCFC 16 602 ATVKVNLPF 16 619 NVDHCLLYH 16 622 HCLLYHREY 16 651 LGDTSPLPP 16 659 PTVPDCLRA 16 673 PSESQKCSF 16 701 TSDSQYDAL 16 89 CVESTRIWM 15 121 QKKDCCADY 15 210 YTIVTGLYP 15 278 INGSFPSIY 15 309 PKAERPRFY 15 321 FEEPDSSGH 15 344 VVDHAFGML 15 419 NSEEIVRNL 15 521 MCDLLRIQP 15 547 FYEPSHAEE 15 585 QLEQVNQML 15 719 EEFRKMWDY 15 851 YQDKVQPVS 15 47 KLEKQGSCR 14 116 SDDCLQKKD 14 273 GSEVAINGS 14 300 STLLKWLDL 14 508 EVEPFENIE 14 646 YTVPQLGDT 14 754 NYDGHFDAP 14 847 GLDFYQDKV 14 V2-HLA-A1-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 82; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 8 QRKDCCADY 15 2 CSDDCLQRK 14 3 SDDCLQRKD 14 9 RKDCCADYK 10 1 SCSDDCLQR 8 V3-HLA-A1-9mers-161P2F108 Each peptide is a portion of SEQ ID NO: 85; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 5 ESCPGGKPE 11 3 NVESCPGGK 10 9 GGKPEALWV 10 1 PTNVESCPG 6 4 VESCPGGKP 5 V4-HLA-A1-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 88; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 1 TYLPTFETP 7 2 YLPTFETPI 3

TABLE XXIII Pos 123456789 score V1-HLA-A0201-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 81; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 179 TLMPNINKL 30 40 GLGLGLRKL 29 723 KMWDYFHSV 25 27 VLLALLVIM 24 29 LALLVIMSL 24 31 LLVIMSLGL 24 215 GLYPESHGI 24 277 AINGSFPSI 24 519 NLMCDLLRI 24 572 SLDCFCPHL 24 33 VIMSLGLGL 23 360 NLHNCVNII 23 847 GLDFYQDKV 23 867 YLPTFETTI 23 23 IACIVLLAL 22 298 RISTLLKWL 22 534 GTHGSLNHL 22 607 NLPFGRPRV 22 768 HLANTDVPI 22 24 ACIVLLALL 21 26 IVLLALLVI 21 223 IIDNNMYDV 21 259 AMYQGLKAA 21 460 HLFVDQQWL 21 592 MLNLTQEEI 21 623 CLLYHREYV 21 21 YKIACIVLL 20 22 KIACIVLLA 20 25 CIVLLALLV 20 65 GLENCRCDV 20 256 WLTAMYQGL 20 300 STLLKWLDL 20 337 RVIKALQVV 20 385 YMTDYFPRI 20 439 YLTPDLPKR 20 537 GSLNHLLKV 20 560 SVCGFANPL 20 600 ITATVKVNL 20 807 IIPHRPTNV 20 836 IARVRDVEL 20 28 LLALLVIMS 19 37 LGLGLGLGL 19 204 KTFPNHYTI 19 451 AKNVRIDKV 19 455 RIDKVHLFV 19 585 QLEQVNQML 19 653 DTSPLPPTV 19 709 LITSNLVPM 19 800 WLDVLPFII 19 5 LTLATEQPV 18 36 SLGLGLGLG 18 285 IYMPYNGSV 18 351 MLMEGLKQR 18 443 DLPKRLHYA 18 682 YLADKNITH 18 731 VLLIKHATE 18 834 AHIARVRDV 18 840 RDVELLTGL 18 860 EILQLKTYL 18 35 MSLGLGLGL 17 38 GLGLGLGLR 17 139 WLEENCDTA 17 165 SMDGFRAEY 17 173 YLYTWDTLM 17 334 VSARVIKAL 17 397 YMYEGPAPR 17 440 LTPDLPKRL 17 462 FVDQQWLAV 17 512 FENIEVYNL 17 538 SLNHLLKVP 17 565 ANPLPTESL 17 595 LTQEEITAT 17 596 TQEEITATV 17 737 ATERNGVNV 17 738 TERNGVNVV 17 799 GWLDVLPFI 17 825 ALWVEERFT 17 850 FYQDKVQPV 17 854 KVQPVSEIL 17 863 QLKTYLPTF 17 34 IMSLGLGLG 16 157 DLPPVILFS 16 208 NHYTIVTGL 16 231 VNLNKNFSL 16 301 TLLKWLDLP 16 330 AGGPVSARV 16 453 NVRIDKVHL 16 520 LMCDLLRIQ 16 646 YTVPQLGDT 16 706 YDALITSNL 16 707 DALITSNLV 16 732 LLIKHATER 16 774 VPIPTHYFV 16 796 NCPGWLDVL 16 806 FIIPHRPTN 16 837 ARVRDVELL 16 861 ILQLKTYLP 16 18 LKKYKIACI 15 104 GETRLEASL 15 107 RLEASLCSC 15 119 CLCKKDCCA 15 132 VCQGETSWL 15 211 TIVTGLYPE 15 305 WLDLPKAER 15 328 GHAGGPVSA 15 340 KALQVVDHA 15 344 VVDHAFGML 15 369 LLADHGMDQ 15 419 NSEEIVRNL 15 496 FLAHGPSFK 15 542 LLKVPFYEP 15 591 QMLNLTQEE 15 594 NLTQEEITA 15 598 EEITATVKV 15 608 LPFGRPRVL 15 615 VLQKNVDHC 15 692 FLYPPASNR 15 708 ALITSNLVP 15 735 KHATERNGV 15 761 APDEITKHL 15 775 PIPTHYFVV 15 803 VIPFIIPHR 15 831 RFTAHLARV 15 843 ELLTGLDFY 15 856 QPVSEILQL 15 865 KTYLPTFET 15 30 ALLVIMSLG 14 42 GLGLRKLEK 14 150 SQCPEGFDL 14 155 GFDLPPVIL 14 191 GIHSKYMRA 14 268 TYFWPGSEV 14 270 FWPGSEVAI 14 284 SIYMPYNGS 14 294 PFEERISTL 14 303 LKWLDLPKA 14 336 ARVIKALQV 14 341 ALQVVDHAF 14 348 AFGMLMEGL 14 350 GMLMEGLKQ 14 362 HNCVNIILL 14 368 ILLADHGMD 14 436 FKPYLTPDL 14 448 LHYAKNVRI 14 524 LLRIQPAPN 14 548 YEPSHAEEV 14 581 QNSTQLEQV 14 588 QVNQMLNLT 14 624 LLYHREYVS 14 640 MPMWSSYTV 14 643 WSSYTVPQL 14 656 PLPPTVPDC 14 661 VPDCLRADV 14 664 CLRADVRVP 14 688 ITHGFLYPP 14 713 NLVPMYEEF 14 716 PMYEEFRKM 14 730 SVLLIKHAT 14 742 GVNVVSGPI 14 764 EITKHLANT 14 776 IPTHYFVVL 14 844 LLTGLDFYQ 14 853 DKVQPVSEI 14 V2-HLA-A0201-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 82; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 6 CLQRKDCCA 15 2 CSDDCLQRK 5 3 SDDCLQRKD 5 V3-HLA-A0201-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 85; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 7 CPGGKPEAL 14 8 SCPGGKPEA 13 9 GGKPEALWV 13 V4-HLA-A0201-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 88; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 2 YLPTFETPI 21

TABLE XXIV Pos 123456789 score V1-HLA-A0203-9mers-161P2F10B No Results Found. V2-HLA-A0203-9mers-161P2F108 No Results Found. V3-HLA-A0203-9mers-161P2F10B No Results Found. V4-HLA-A0203-9mers-161P2F10B No Results Found.

TABLE XXV Pos 123456789 score V1-HLA-A3-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 81; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 670 RVPPSESQK 33 496 FLAHGPSFK 27 692 FLYPPASNR 27 42 GLGLRKLEK 26 423 IVRNLSCRK 26 6 TLATEQPVK 25 614 RVLQKNVDH 25 12 PVKKNTLKK 24 302 LLKWLDLPK 24 610 FGRPRVLQK 24 47 KLEKQGSCR 23 708 ALITSNLVP 23 26 IVLLALLVI 22 447 RLHYAKNVR 22 782 VVLTSCKNK 22 838 RVRDVELLT 22 337 RVIKALOVV 21 405 RIRAHNIPH 21 469 AVRSKSNTN 21 597 QEEITATVK 21 628 REYVSGFGK 21 682 YLADKNITH 21 731 VLLIKHATE 21 732 LLIKHATER 21 814 NVESCPEGK 21 857 PVSEILQLK 21 863 QLKTYLPTF 21 39 LGLGLGLRK 20 351 MLMEGLKQR 20 624 LLYHREYVS 20 843 ELLTGLDFY 20 196 YMRAMYPTK 19 227 NMYDVNLNK 19 338 VIKALQVVD 19 341 ALQVVDHAF 19 544 KVPFYEPSH 19 664 CLRADVRVP 19 802 DVLPFIIPH 19 806 FIIPHRPTN 19 827 WVEERFTAH 19 27 VLLALLVIM 18 30 ALLVIMSLG 18 38 GLGLGLGLR 18 107 RLEASLCSC 18 114 SCSDDCLQK 18 261 YQGLKAATY 18 275 EVAINGSFP 18 306 WLDLPKAER 18 368 ILLADHGMD 18 422 EIVRNLSCR 18 453 NVRIDKVHL 18 524 LLRIQPAPN 18 550 PSHAEEVSK 18 745 VVSGPIFDY 18 759 FDAPDEITK 18 835 HIARVRDVE 18 157 DLPPVILFS 17 162 ILFSMDGFR 17 186 KLKTCGIHS 17 215 GLYPESHGI 17 296 EERISTLLK 17 439 YLTPDLPKR 17 458 KVHLFVDQQ 17 619 NVDHCLLYH 17 647 TVPQLGDTS 17 668 DVRVPPSES 17 713 NLVPMYEEF 17 854 KVQPVSEIL 17 7 LATEQPVKK 16 44 GLRKLEKQG 16 68 NCRCDVACK 16 94 RIWMCNKFR 16 122 KKDCCADYK 16 131 SVCQGETSW 16 343 QVVDHAFGM 16 355 GLKQRNLHN 16 369 LLADHGMDQ 16 442 PDLPKRLHY 16 455 RIDKVHLFV 16 498 AHGPSFKEK 16 523 DLLRIQPAP 16 526 RIQPAPNNG 16 560 SVCGFANPL 16 630 YVSGFGKAM 16 678 KCSFYLADK 16 698 SNRTSDSQY 16 768 HLANTDVPI 16 V2-HLA-A3-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 82; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 9 RKDCCADYK 17 6 CLQRKDCCA 14 8 QRKDCCADY 13 1 SCSDDCLQR 12 2 CSDDCLQRK 11 V3-HLA-A3-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 85; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 3 NVESCPGGK 22 9 GGKPEALWV 11 V4-HLA-A3-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 88; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 2 YLPTFETPI 11

TABLE XXVI Pos 123456789 score V1-HLA-A26-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 81; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 510 EPFENIEVY 31 516 EVYNLMCDL 29 773 DVPIPTHYF 26 388 DYFPRINFF 25 719 EEFRKMWDY 25 422 EIVRNLSCR 24 710 ITSNLVPMY 24 745 VVSGPIFDY 24 802 DVLPFIIPH 24 843 ELLTGLDFY 24 275 EVAINGSFP 23 587 EQVNQMLNL 23 860 EILQLKIYL 23 167 DGFRAEYLY 22 188 KTCGIHSKY 22 297 ERISTLLKW 21 312 ERPRFYTMY 21 508 EVEPFENIE 21 602 ATVKVNLPF 21 10 EQPVKKNTL 20 344 VVDHAFGML 20 534 GTHGSLNHL 20 555 EVSKFSVCG 20 841 DVELLTGLD 20 859 SEILQLKTY 20 32 LVIMSLGLG 19 72 DVACKDRGD 19 105 ETRLEASLC 19 136 ETSWLEENC 19 172 EYLYTWDTL 19 230 DVNLNKNFS 19 300 STLLKWLDL 19 377 QTYCNKMEY 19 488 EFRSMEAIF 19 560 SVCGFANPL 19 599 EITATVKVN 19 653 DTSPLPP1V 19 668 DVRVPPSES 19 764 EITKHLANT 19 840 RDVELLTGL 19 854 KVQPVSEIL 19 856 QPVSEILQL 19 202 PTKTFPNHY 18 337 RVIKALQVV 18 364 CVNIILLAD 18 440 LTPDLPKRL 18 453 NVRIDKVHL 18 454 VRIDKVHLF 18 646 YTVPQLGDT 18 675 ESQKCSFYL 18 720 EFRKMWDYF 18 772 TDVPIPTHY 18 824 EALWVEERF 18 857 PVSEILQLK 18 24 ACIVLLALL 17 77 DRGDCCWDF 17 178 DTLMPNINK 17 274 SEVAINGSF 17 298 RISTLLKWL 17 551 SHAEEVSKF 17 554 EEVSKFSVC 17 629 EYVSGFGKA 17 660 TVPDCLRAD 17 685 DKNITHGFL 17 726 DYFHSVLLI 17 853 DKVQPVSEI 17 2 ESTLTLATE 16 21 YKIACIVLL 16 33 VIMSLGLGL 16 87 DTCVESTRI 16 145 DTAQQSQCP 16 154 EGFDLPPVI 16 179 TLMPNINKL 16 219 ESHGIIDNN 16 225 DNNMVDVNL 16 294 PFEERISTL 16 333 PVSARVIKA 16 419 NSEEIVRNL 16 421 EEIVRNLSC 16 513 ENIEVYNLM 16 600 ITATVKVNL 16 603 TVKVNLPFG 16 618 KNVDHCLLY 16 744 NVVSGPIFD 16 830 ERFTAHIAR 16 837 ARVRDVELL 16 13 VKKNTLKKY 15 26 IVLLALLVI 15 204 KTFPNHYTI 15 221 HGIIDNNMY 15 343 QVVDHAFGM 15 391 PRINFFYMY 15 458 KVHLFVDQQ 15 493 EAIFLAHGP 15 540 NHLLKVPFY 15 568 LPTESLDCF 15 595 LTQEEITAT 15 598 EEITATVKV 15 619 NVDHCLLYH 15 626 YHREYVSGF 15 686 KNITHGFLY 15 763 DEITKHLAN 15 781 FVVLTSCKN 15 V2-HLA-A26-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 82; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 8 QRKDCCADY 11 4 DDCLQRKDC 8 5 DCLQRKDCC 8 2 CSDDCLQRK 5 V3-HLA-A26-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 85; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 3 NVESCPGGK 12 5 ESCPGGKPE 12 7 CPGGKPEAL 10 1 PTNVESCPG 8 2 TNVESCPGG 7 V4-HLA-A26-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 88; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 1 TYLPTFETP 3

TABLE XXVII Pos 123456789 score V1-HLA-B0702-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 81; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 776 IPTHYFVVL 25 761 APDEITKHL 24 608 LPFGRPRVL 23 818 CPEGKPEAL 23 856 QPVSEILQL 22 313 RPRFYTMYF 20 403 APRIRAHNI 20 657 LPPTVPDCL 20 793 TPENCPGWL 20 287 MPYNGSVPF 19 308 LPKAERPRF 19 390 FPRINFFYM 19 612 RPRVLQKNV 19 661 VPDCLRADV 19 181 MPNINKLKT 18 206 FPNHYTIVT 18 655 SPLPPTVPD 18 774 VPIPTHYFV 18 293 VPFEERIST 17 640 MPMWSSYTV 17 155 GFDLPPVIL 16 158 LPPVILFSM 16 545 VPFYEPSHA 16 565 ANPLPTESL 16 568 LPTESLDCF 16 808 IPHRPTNVE 16 35 MSLGLGLGL 15 37 LGLGLGLGL 15 152 CPEGFDLPP 15 836 IARVRDVEL 15 23 IACIVLLAL 14 33 VIMSLGLGL 14 100 KFRCGETRL 14 323 EPDSSGHAG 14 431 KPDQHFKPY 14 441 TPDLPKRLH 14 453 NVRIDKVHL 14 549 EPSHAEEVS 14 600 ITATVKVNL 14 643 WSSYTVPQL 14 649 PQLGDTSPL 14 822 KPEALWVEE 14 21 YKIACIVLL 13 24 ACIVLLALL 13 58 CFDASFRGL 13 132 VCQGETSWL 13 201 YPTKTFPNH 13 253 QPMWLTAMY 13 271 WPGSEVAIN 13 282 FPSIYMPYN 13 298 RISTLLKWL 13 332 GPVSARVIK 13 348 AFGMLMEGL 13 401 GPAPRIRAH 13 411 IPHDFFSFN 13 489 FRSMEAIFL 13 530 APNNGTHGS 13 560 SVCGFANPL 13 587 EQVNQMLNL 13 658 PPTVPDCLR 13 695 PPASNRTSD 13 796 NCPGWLDVL 13 797 CPGWLDVLP 13 837 ARVRDVELL 13 1 MESTLTLAT 12 11 OPVKKNTLK 12 20 KYKIACIVL 12 31 LLVIMSLGL 12 112 LCSCSDDCL 12 150 SQCPEGFDL 12 179 TLMPNINKL 12 198 RAMYPTKTF 12 208 NHYTIVTGL 12 225 DNNMYDVNL 12 249 WWHGQPMWL 12 277 AINGSFPSI 12 300 STLLKWLDL 12 311 AERPRFYTM 12 334 VSARVIKAL 12 344 VVDHAFGML 12 398 MYEGPAPRI 12 400 EGPAPRIRA 12 408 AHNIPHDFF 12 428 SCRKPDQHF 12 436 FKPYLTPDL 12 455 RIDKVHLFV 12 500 GPSFKEKTE 12 510 EPFENIEVY 12 528 QPAPNNGTH 12 531 PNNGTHGSL 12 534 GTHGSLNHL 12 572 SLDCFCPHL 12 602 ATVKVNLPF 12 630 YVSGFGKAM 12 672 PPSESQKCS 12 675 ESQKCSFYL 12 701 TSDSQYDAL 12 706 YDALITSNL 12 724 MWDYFHSVL 12 725 WDYFHSVLL 12 840 RDVELLTGL 12 854 KVQPVSEIL 12 860 EILQLKTYL 12 V2-B0702-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 82; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 6 CLQRKDCCA 6 1 SCSDDCLQR 4 7 LQRKDCCAD 4 9 RKDCCADYK 2 2 CSDDCLQRK 1 3 SDDCLQRKD 1 4 DDCLORKDC 1 8 QRKDCCADY 1 V3-HLA-B0702-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 85; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 7 CPGGKPEAL 24 V4-HLA-B0702-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 88; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 2 YLPTFETPI 8

TABLE XXVIII Pos 123456789 score V1-HLA-B08-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 81; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 836 IARVRDVEL 32 18 LKKYKIACI 28 184 INKLKTCGI 28 818 CPEGKPEAL 27 355 GLKQRNLHN 26 403 APRIRAHNI 26 502 SFKEKTEVE 24 608 LPFGRPRVL 24 10 EQPVKKNTL 23 300 STLLKWLDL 23 231 VNLNKNFSL 22 308 LPKAERPRF 22 786 SCKNKSHTP 22 863 QLKTYLPTF 22 294 PFEERISTL 21 353 MEGLKQRNL 21 20 KYKIACIVL 20 616 LQKNVDHCL 20 98 CNKFRCGET 19 761 APDEITKHL 19 40 GLGLGLRKL 18 53 SCRKKCFDA 18 74 ACKDRGDCC 18 166 MDGFRAEYL 18 238 SLSSKEQNN 18 313 RPRFYTMYF 18 448 LHYAKNVRI 18 454 VRIDKVHLF 18 460 HLFVDQQWL 18 500 GPSFKEKTE 18 542 LLKVPFYEP 18 556 VSKFSVCGF 18 572 SLDCFCPHL 18 776 IPTHYYFWL 18 861 ILOLKTYLP 18 11 QPVKKNTLK 17 15 KNTLKKYKI 17 17 TLKKYKIAC 17 42 GLGLRKLEK 17 179 TLMPNINKL 17 263 GLKAATYFW 17 401 GPAPRIRAH 17 444 LPKRLHYAK 17 453 NVRIDKVHL 17 504 KEKTEVEPF 17 585 QLEQVNQML 17 682 YLADKNITH 17 731 VLLIKHATE 17 856 QPVSEILQL 17 23 IACIVLLAL 16 29 LALLVIMSL 16 31 LLVIMSLGL 16 55 RKKCFDASF 16 100 KFRCGETRL 16 119 CLQKKDCCA 16 126 CADYKSVCQ 16 186 KLKFCGIHS 16 256 WLTAMYQGL 16 302 LLKWLDLPK 16 338 VIKALQVVD 16 467 WLAVRSKSN 16 469 AVRSKSNTN 16 601 TATVKVNLP 16 610 FGRPRVLQK 16 657 LPPTVPDCL 16 684 ADKNITHGF 16 736 HATERNGVN 16 793 TPENCPGWL 16 860 EILQLKTYL 16 33 VIMSLGLGL 15 51 QGSCRKKCF 15 191 GIHSKYMRA 15 240 SSKEQNNPA 15 298 RISTLLKWL 15 388 DYFPRINFF 15 626 YHREYVSGF 15 V2-B08-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 82; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 6 CLQRKDCCA 16 8 QRKDCCADY 10 5 DCLQRKDCC 8 7 LQRKDCCAD 7 V3-HLA-B08-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 85; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 7 CPGGKPEAL 27 V4-HLA-B08-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 88; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 2 YLPTFETPI 12

TABLE XXIX Pos 123456789 score V1-HLA-B1510-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 81; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 192 IHSKYMRAM 24 578 PHLQNSTQL 22 208 NHYTIVTGL 21 535 THGSLNHLL 21 361 LHNCVNIIL 20 551 SHAEEVSKF 19 626 YHREYVSGF 19 328 GHAGGPVSA 17 408 AHNIPHDFF 17 220 SHGIIDNNM 16 600 ITATVKVNL 16 608 LPFGRPRVL 16 776 IPTHYFVVL 16 836 IARVRDVEL 16 155 GFDLPPVIL 15 179 TLMPNINKL 15 419 NSEEIVRNL 15 809 PHRPTNVES 15 10 EQPVKKNTL 14 21 YKIACIVLL 14 40 GLGLGLRKL 14 294 PFEERISTL 14 440 LTPDLPKRL 14 448 LHYAKNVRI 14 757 GHFDAPDEI 14 818 CPEGKPEAL 14 23 IACIVLLAL 13 100 KFRCGETRL 13 250 WHGQPMWLT 13 334 VSARVIKAL 13 346 DHAFGMLME 13 362 HNCVNIILL 13 434 QHFKPYLTP 13 453 NVRIDKVHL 13 498 AHGPSFKEK 13 643 WSSYTVPQL 13 767 KNLANTDVP 13 778 THYFVVLTS 13 793 TPENCPGWL 13 796 NCPGWLDVL 13 834 AHIARVRDV 13 860 EILQLKTYL 13 20 KYKIACIVL 12 58 CFDASFRGL 12 150 SQCPEGFDL 12 172 EYLYFWDTL 12 225 DNNMYDVNL 12 249 WWHGQPMWL 12 353 MEGLKQRNL 12 432 PDQHFKPYL 12 516 EVYNLMCDL 12 534 GTHGSLNHL 12 540 NHLLKVPFY 12 585 QLEQVNQML 12 587 EQVNQMLNL 12 621 DHCLLYHRE 12 675 ESQKCSFYL 12 689 THGFLYPPA 12 701 TSDSQYDAL 12 706 YDALITSNL 12 724 MWDYFHSVL 12 725 WDYFHSVLL 12 728 FHSVLLIKH 12 735 KHATERNGV 12 791 SHTPENCPG 12 854 KVQPVSEIL 12 24 ACIVILALL 11 29 LALLVIMSL 11 35 MSLGLGLGL 11 37 LGLGLGLGL 11 104 GETRLEASL 11 112 LCSCSDDCL 11 132 VCQGETSWL 11 295 FEERISTLL 11 298 RISTLLKWL 11 348 AFGMLMEGL 11 436 FKPYLTPDL 11 460 HLFVDQQWL 11 482 NHGYNNEFR 11 489 FRSMEAIFL 11 512 FENIEVYNL 11 531 PNNGTHGSL 11 560 SVCGFANPL 11 565 ANPLPTESL 11 572 SLDCFCPHL 11 617 QKNVDHCLL 11 649 PQLGDTSPL 11 657 LPPTVPDCL 11 761 APDEITKHL 11 837 ARVRDVELL 11 840 RDVELLTGL 11 856 QPVSEILQL 11 V2-B1510-9mers: 161P2F10B Each peptide is a portion of SEQ ID NO: 82; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 2 CSDDCLQRK 3 1 SCSDDCLQR 2 3 SDDCLQRKD 2 5 DCLQRKDCC 2 7 LQRKDCCAD 2 4 DDCLQRKDC 1 8 QRKDCCADY 1 V3-HLA-B1510-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 85; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 7 CPGGKPEAL 13 V4-HLA-B1510-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 88; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 1 TYLPTFETP 4 2 YLPTFETPI 1

TABLE XXX Pos 123456789 score V1-HLA-B2705-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 81; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 93 TRIWMCNKF 25 454 VRIDKVHLF 24 830 ERFTAHIAR 24 429 CRKPDQHFK 23 489 FRSMEAIFL 23 837 ARVRDVELL 23 77 DRGDCCWDF 21 391 PRINFFYMY 21 638 MRMPMWSSY 21 312 ERPRFYTMY 20 721 FRKMWDYFH 20 840 RDVELLTGL 20 29 LALLVIMSL 19 40 GLGLGLRKL 19 525 LRIQPAPNN 19 614 RVLQKNVDH 19 39 LGLGLGLRK 18 100 KFRCGETRL 18 388 DYFPRINFF 18 470 VRSKSNTNC 18 481 GNHGYNNEF 18 534 GTHGSLNHL 18 578 PHLQNSTQL 18 632 SGFGKAMRM 18 670 RVPPSESQK 18 692 FLYPPASNR 18 732 LLIKHATER 18 860 EILQLKTYL 18 11 QPVKKNTLK 17 38 GLGLGLGLR 17 42 GLGLRKLEK 17 48 LEKQGSCRK 17 55 RKKCFDASF 17 178 DTLMPNINK 17 179 TLMPNINKL 17 227 NMYDVNLNK 17 262 QGLKAATYF 17 374 GMDQTYCNK 17 446 KRLHYAKNV 17 447 RLHYAKNVR 17 602 ATVKVNLPF 17 611 GRPRVLQKN 17 628 REYVSGFGK 17 856 QPVSEILQL 17 21 YKIACIVLL 16 24 ACIVLLALL 16 35 MSLGLGLGL 16 37 LGLGLGLGL 16 104 GETRLEASL 16 155 GFDLPPVIL 16 156 FDLPPVILF 16 187 LKTCGIHSK 16 188 KTCGIHSKY 16 198 RAMYPTKTF 16 208 NHYTIVTGL 16 287 MPYNGSVPF 16 294 PFEERISTL 16 297 ERISTLLKW 16 298 RISTLLKWL 16 336 ARVIKALQV 16 353 MEGLKQRNL 16 387 TDYFPRINF 16 397 YMYEGPAPR 16 510 EPFENIEVY 16 551 SHAEEVSKF 16 600 ITATVKVNL 16 608 LPFGRPRVL 16 739 ERNGVNVVS 16 760 DAPDEITKH 16 6 TLATEQPVK 15 12 PVKKNTLKK 15 47 KLEKQGSCR 15 49 EKQGSCRKK 15 63 FRGLENCRC 15 94 RIWMCNKFR 15 106 TRLEASLCS 15 162 ILFSMDGFR 15 190 CGIHSKYMR 15 229 YDVNLNKNF 15 231 VNLNKNFSL 15 300 STLLKWLDL 15 305 WLDLPKAER 15 313 RPRFYTMYF 15 329 HAGGPVSAR 15 332 GPVSARVIK 15 351 MLMEGIKQR 15 359 RNLHNCVNI 15 401 GPAPRIRAH 15 406 IRAHNIPHD 15 407 RAHNIPHDF 15 419 NSEEIVRNL 15 423 IVRNLSCRK 15 438 PYLTPDLPK 15 439 YLTPDLPKR 15 460 HLFVDQQWL 15 463 VDQQWLAVR 15 495 IFLAHGPSF 15 512 FENIEVYNL 15 613 PRVLQKNVD 15 649 PQLGDTSPL 15 669 VRVPPSESQ 15 706 YDALITSNL 15 782 VVLTSCKNK 15 802 DVLPFIIPH 15 803 VLPFIIPHR 15 824 EALWVEERF 15 854 KVQPVSEIL 15 7 LATEQPVKK 14 10 EQPVKKNTL 14 14 KKNTLKKYK 14 15 KNTLKKYKI 14 20 KYKIACIVL 14 23 IACIVLLAL 14 56 KKCFDASFR 14 62 SFRGLENCR 14 69 CRCDVACKD 14 70 RCDVACKDR 14 99 NKFRCGETR 14 132 VCQGETSWL 14 169 FRAEYLYTW 14 197 MRAMYPTKT 14 204 KTFPNHYTI 14 215 GLYPESHGI 14 225 DNNMYDVNL 14 234 NKNFSLSSK 14 252 GQPMWLTAM 14 274 SEVAINGSF 14 295 FEERISTLL 14 308 LPKAERPRF 14 314 PRFYTMYPE 14 334 VSARVIKAL 14 362 HNCVNIILL 14 405 RIRAHNIPH 14 424 VRNLSCRKP 14 428 SCRKPDQHF 14 452 KNVRIDKVH 14 498 AHGPSFKEK 14 504 KEKTEVEPF 14 518 YNLMCDLLR 14 533 NGTHGSLNH 14 539 LNHLLKVPF 14 540 NHLLKVPFY 14 560 SVCGFANPL 14 565 ANPLPTESL 14 584 TQLEQVNQM 14 585 QLEQVNQML 14 587 EQVNOMLNL 14 597 QEEITATVK 14 610 FGRPRVLQK 14 631 VSGFGKAMR 14 678 KCSFYLADK 14 716 PMYEEFRKM 14 725 WDYFHSVLL 14 745 VVSGPIFDY 14 771 NTDVPIPTH 14 796 NCPGWLDVL 14 799 GWLDVLPFI 14 836 IARVRDVEL 14 839 VRDVELLTG 14 842 VELLTGLDF 14 26 IVLLALLVI 13 27 VLLALLVIM 13 31 LLVIMSLGL 13 45 LRKLEKQGS 13 86 EDTCVESTR 13 101 FRCGETRLE 13 115 CSDDCLQKK 13 122 KKDCCADYK 13 161 VILFSMDGF 13 172 EYLYTWDTL 13 173 YLYTWDTLM 13 201 YPTKTFPNH 13 220 SHGIIDNNM 13 249 WWHGQPMWL 13 261 YQGLKAATY 13 291 GSVPFEERI 13 302 LLKWLDLPK 13 341 ALQVVDHAF 13 354 EGLKQRNLH 13 358 QRNLHNCVN 13 361 LHNCVNIIL 13 365 VNIILLADH 13 367 IILLADHGM 13 371 ADHGMDQTY 13 377 QTYCNKMEY 13 398 MYEGPAPRI 13 404 PRIRAHNIP 13 417 SFNSEEIVR 13 422 EIVRNLSCR 13 440 LTPDLPKRL 13 442 PDLPKRLHY 13 448 LHYAKNVRI 13 465 QQWLAVRSK 13 477 NCGGGNHGY 13 484 GYNNEFRSM 13 496 FLAHGPSFK 13 513 ENIEVYNLM 13 516 EVYNLMCDL 13 531 PNNGTHGSL 13 550 PSHAEEVSK 13 568 LPTESLDCF 13 606 VNLPFGRPR 13 620 VDHCLLYHR 13 626 YHREYVSGF 13 643 WSSYIVPQL 13 662 PDCLRADVR 13 675 ESQKCSFYL 13 713 NLVPMYEEF 13 715 VPMYEEFRK 13 719 EEFRKMWDY 13 727 YFHSVLLIK 13 728 FHSVLLIKH 13 743 VNVVSGPIF 13 751 FDYNYDGHF 13 757 GHFDAPDEI 13 759 FDAPDEITK 13 761 APDEITKHL 13 772 TDVPIPTHY 13 776 IPTHYFVVL 13 780 YFVVLTSCK 13 798 PGWLDVLPF 13 818 CPEGKPEAL 13 823 PEALWVEER 13 832 FTAHIARVR 13 843 ELLTGLDFY 13 853 DKVQPVSEI 13 857 PVSEILQLK 13 859 SEILQLKTY 13 863 QLKTYLPTF 13 33 VIMSLGLGL 12 54 CRKKCFDAS 12 68 NCRCDVACK 12 87 DTCVESTRI 12 92 STRIWMCNK 12 112 LCSCSDDCL 12 114 SCSDDCLQK 12 148 QQSQCPEGF 12 150 SQCPEGFDL 12 154 EGFDLPPVI 12 165 SMDGFRAEY 12 167 DGFRAEYLY 12 180 LMPNINKLK 12 185 NKLKTCGIH 12 196 YMRAMYPTK 12 221 HGIIDNNMY 12 257 LTAMYQGLK 12 277 AINGSFPSI 12 280 GSFPSIYMP 12 290 NGSVPFEER 12 296 EERISTLLK 12 307 DLPKAERPR 12 311 AERPRFYTM 12 331 GGPVSARVI 12 339 IKALQVVDH 12 348 AFGMLMEGL 12 382 KMEYMTDYF 12 408 AHNIPHDFF 12 431 KPDQHFKPY 12 432 PDQHFKPYL 12 436 FKPYLTPDL 12 444 LPKRLHYAK 12 450 YAKNVRIDK 12 453 NVRIDKVHL 12 475 NTNCGGGNH 12 535 THGSLNHLL 12 536 HGSLNHLLK 12 544 KVPFYEPSH 12 556 VSKFSVCGF 12 604 VKVNLPFGR 12 616 LQKNVDHCL 12 618 KNVDHCLLY 12 622 HCLLYHREY 12 627 HREYVSGFG 12 658 PPTVPDCLR 12 665 LRADVRVPP 12 673 PSESQKCSF 12 674 SESQKCSFY 12 680 SFYLADKNI 12 682 YLADKNITH 12 684 ADKNITHGF 12 686 KNITHGFLY 12 698 SNRTSDSQY 12 710 ITSNLVPMY 12 720 EFRKMWDYF 12 724 MWDYFHSVL 12 726 DYFHSVLLI 12 747 SGPIFDYNY 12 810 HRPTNVESC 12 846 TGLDFYQDK 12 V2-HLA-B2705-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 82; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 8 QRKDCCADY 19 9 RKDCCADYK 15 2 CSDDCLQRK 13 1 SCSDDCLQR 12 V3-HLA-B2705-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 85; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 7 CPGGKPEAL 13 3 NVESCPGGK 10 6 SCPGGKPEA 7 V4-HLA-B2705.9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 88; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 2 YLPTFETPI 8 1 TYLPTFETP 4

TABLE XXXI Pos 123456789 score V1-HLA-B2709-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 81; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 446 KRLHYAKNV 24 837 ARVRDVELL 24 336 ARVIKALQV 23 489 FRSMEAIFL 21 454 VRIDKVHLF 20 93 TRIWMCNKF 19 77 DRGDCCWDF 18 359 RNLHNCVNI 16 840 RDVELLTGL 15 19 KKYKIACIV 14 104 GETRLEASL 14 155 GFDLPPVIL 14 204 KTFPNHYTI 14 208 NHYTIVTGL 14 215 GLYPESHGI 14 291 GSVPFEERI 14 298 RISTLLKWL 14 525 LRIQPAPNN 14 537 GSLNHLLKV 14 799 GWLDVLPFI 14 831 RFTAHIARV 14 856 QPVSEILQL 14 35 MSLGLGLGL 13 37 LGLGLGLGL 13 40 GLGLGLRKL 13 100 KFRCGETRL 13 106 TRLEASLCS 13 297 ERISTLLKW 13 300 STLLKWLDL 13 314 PRFYTMYFE 13 337 RVIKALQVV 13 407 RAHNIPHDF 13 419 NSEEIVRNL 13 455 RIDKVHLFV 13 460 HLFVDQQWL 13 512 FENIEVYNL 13 534 GTHGSLNHL 13 578 PHLQNSTQL 13 587 EQVNQMLNL 13 600 ITATVKVNL 13 611 GRPRVLQKN 13 612 RPRVLQKNV 13 643 WSSYTVPQL 13 649 PQLGDTSPL 13 699 NRTSDSQYD 13 725 WDYFHSVLL 13 757 GHFDAPDEI 13 776 IPTHYFVVL 13 854 KVQPVSEIL 13 15 KNTLKKYKI 12 20 KYKIACIVL 12 21 YKIACIVLL 12 23 IACIVLLAL 12 24 ACIVLLALL 12 26 IVLLALLVI 12 29 LALLVIMSL 12 31 LLVIMSLGL 12 33 VIMSLGLGL 12 55 RKKCFDASF 12 156 FDLPPVILF 12 172 EYLYTWDTL 12 198 RAMYPTKTF 12 225 DNNMYDVNL 12 231 VNLNKNFSL 12 313 RPRFYTMYF 12 331 GGPVSARVI 12 391 PRINFFYMY 12 406 IRAHNIPHD 12 429 CRKPDQHFK 12 448 LHYAKNVRI 12 453 NVRIDKVHL 12 495 IFLAHGPSF 12 516 EVYNLMCDL 12 584 TQLEQVNQM 12 608 LPFGRPRVL 12 632 SGFGKAMRM 12 663 DCLRADVRV 12 669 VRVPPSESQ 12 706 YDALITSNL 12 726 DYFHSVLLI 12 761 APDEITKHL 12 830 ERFTAHIAR 12 836 IARVRDVEL 12 860 EILQLKTYL 12 25 CIVLLALLV 11 27 VLLALLVIM 11 63 FRGLENCRC 11 65 GLENCRCDV 11 69 CRCDVACKD 11 150 SQCPEGFDL 11 154 EGFDLPPVI 11 166 MDGFRAEYL 11 169 FRAEYLYTW 11 179 TLMPNINKL 11 252 GQPMWLTAM 11 256 WLTAMYQGL 11 262 QGLKAATYF 11 287 MPYNGSVPF 11 295 FEERISTLL 11 311 AERPRFYTM 11 330 AGGPVSARV 11 348 AFGMLMEGL 11 353 MEGLKQRNL 11 367 IILLADHGM 11 385 YMTDYFPRI 11 387 TDYFPRINF 11 388 DYFPRINFF 11 398 MYEGPAPRI 11 403 APRIRAHNI 11 404 PRIRAHNIP 11 432 PDQHFKPYL 11 436 FKPYLTPDL 11 440 LTPDLPKRL 11 470 VRSKSNTNC 11 481 GNHGYNNEF 11 484 GYNNEFRSM 11 504 KEKTEVEPF 11 519 NIMCDLLRI 11 535 THGSLNHLL 11 560 SVCGFANPL 11 565 ANPLPTESL 11 572 SLDCFCPHL 11 602 ATVKVNLPF 11 613 PRVLQKNVD 11 617 QKNVDHCLL 11 638 MRMPMWSSY 11 665 LRADVRVPP 11 680 SFYLADKNI 11 701 TSDSQYDAL 11 709 LITSNLVPM 11 721 FRKMWDYFH 11 737 ATERNGVNV 11 739 ERNGVNVVS 11 742 GVNVVSGPI 11 774 VPIPTHYFV 11 798 PGWLDVLPF 11 810 HRPTNVESC 11 820 EGKPEALWV 11 824 EALWVEERF 11 834 AHIARVRDV 11 839 VRDVELLTG 11 842 VELLTGLDF 11 847 GLDFYQDKV 11 V2-HLA-B2709-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 82; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 8 QRKDCCADY 10 9 RKDCCADYK 5 V3-HLA-B2709-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 85; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 9 GGKPEALWV 14 7 CPGGKPEAL 10 V4-HLA-B2709-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 88; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 2 YLPTFETPI 8 1 TYLPTFETP 3

TABLE XXXII Pos 123456789 score V1-HLA-B4402-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 81; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 859 SEILQLKTY 29 719 EEFRKMWDY 25 242 KEQNNPAWW 24 487 NEFRSMEAI 24 295 FEERISTLL 23 504 KEKTEVEPF 23 842 VELLTGLDF 23 274 SEVAINGSF 22 353 MEGLKQRNL 22 674 SESQKCSFY 22 104 GETRLEASL 21 512 FENIEVYNL 21 819 PEGKPEALW 21 179 TLMPNINKL 20 388 DYFPRINFF 20 828 VEERFTAHI 20 311 AERPRFYTM 19 507 TEVEPFENI 19 510 EPFENIEVY 19 598 EEITATVKV 19 21 YKIACIVLL 18 24 ACIVLLALL 18 297 ERISTLLKW 18 334 VSARVIKAL 18 761 APDEITKHL 18 156 FDLPPVILF 17 421 EEIVRNLSC 17 454 VRIDKVHLF 17 608 LPFGRPRVL 17 684 ADKNITHGF 17 763 DEITKHLAN 17 1 MESTLTLAT 16 90 VESTRIWMC 16 204 KTFPNHYTI 16 341 ALQWDIIAF 16 362 HNCVNIILL 16 442 PDLPKRLHY 16 565 ANPLPTESL 16 686 KNITHGFLY 16 837 ARVRDVELL 16 9 TEOPVKKNT 15 10 EQPVKKNTL 15 13 VKKNTLKKY 15 29 LALLVIMSL 15 93 TRIWMCNKF 15 154 EGFDLPPVI 15 171 AEYLYIWDT 15 198 RAMYPTKTF 15 218 PESHGIIDN 15 294 PFEERISTL 15 296 EERISTLLK 15 298 RISTLLKWL 15 371 ADHGMDQTY 15 391 PRINFFYMY 15 399 YEGPAPRIR 15 431 KPDQIFKPY 15 440 LTPDLPKRL 15 745 VVSGPIFDY 15 772 TDVPIPTHY 15 796 NCPGWLDVL 15 843 ELLTGLDFY 15 856 ELLTGLDFY 15 23 IACIVLLAL 14 40 GLGLGLRKL 14 51 QGSCRKKCF 14 141 EENCDTAQQ 14 150 SQCPEGFDL 14 155 GFDLPPVIL 14 165 SMDGFRAEY 14 167 DGFRAEYLY 14 172 EYLYTWDTL 14 188 KTCGIHSKY 14 208 NHYTIVTGL 14 221 HGIIDNNMY 14 241 SKEQNNPAW 14 300 STLLKWLDL 14 312 ERPRFYTMY 14 322 EEPDSSGHA 14 403 APRIRAHNI 14 407 RAHNIPHDF 14 419 NSEEIVRNL 14 420 SEEIVRNLS 14 540 NHLLKVPFY 14 554 EEVSKFSVC 14 560 SVCGFANPL 14 587 EQVNQMLNL 14 602 ATVKVNLPF 14 618 KNVDHCLLY 14 638 MRMPMWSSY 14 713 NLVPMYEEF 14 738 TERNGVNVV 14 818 CPEGKPEAL 14 829 EERFTAHIA 14 854 KVQPVSEIL 14 V2-HLA-B4402-9MERS-161P2F10B Each peptide is a portion of SEQ ID NO: 82; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 8 QRKDCCADY 11 1 SCSDDCLQR 5 V3-HLA-B4402-9MERS-161P2F10B Each peptide is a portion of SEQ ID NO: 85; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. CPGGKPEAL 14 4 VESCPGGKP 12 8 PGGKPEALW 11 5 ESCPGGKPE 7 V4-HLA-B4402-9MERS-161P2F10B Each peptide is a portion of SEQ ID NO: 88; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 2 YLPTFETPI 10 1 TYLPTFETP 6

TABLE XXXIIII Pos 123456789 score V1-HLA-B5101-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 81; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 707 DALITSNLV 26 608 LPFGRPRVL 25 776 IPTHYFVVL 24 29 LALLVIMSL 23 331 GGPVSARVI 23 657 LPPTVPDCL 23 23 IACIVLLAL 22 154 EGFDLPPVI 22 640 MPMWSSYTV 22 403 APRIRAHNI 21 448 LHYAKNVRI 21 760 DAPDEITKH 20 761 APDEITKHL 20 774 VPIPTHYFV 20 26 IVLLALLVI 19 612 RPRVLQKNV 19 661 VPDCLRADV 19 694 YPPASNRTS 19 726 DYFHSVLLI 19 818 CPEGKPEAL 19 836 IARVRDVEL 19 7 LATEQPVKK 18 37 LGLGLGLGL 18 793 TPENCPGWL 18 856 QPVSEILQL 18 330 AGGPVSARV 17 340 KALQVVDHA 17 510 EPFENIEVY 17 867 YLPTFETTI 17 87 DTCVESTRI 16 206 FPNHYTIVT 16 216 LYPESHGII 16 287 MPYNGSVPF 16 385 YMTDYFPRI 16 437 KPYLTPDLP 16 568 LPTESLDCF 16 663 DCLRADVRV 16 683 LADKNITHG 16 736 HATERNGVN 16 799 GWLDVLPFI 16 808 IPHRPTNVE 16 820 EGKPEALWV 16 853 DKVQPVSEI 16 60 DASFRGLEN 15 201 YPTKTFPNH 15 208 NHYTIVTGL 15 270 FWPGSEVAI 15 293 VPFEERIST 15 450 YAKNVRIDK 15 497 LAHGPSFKE 15 552 HAEEVSKFS 15 601 TATVKVNLP 15 653 DTSPLPPTV 15 680 SFYLADKNI 15 738 TERNGVNVV 15 769 LANTDVPIP 15 804 LPFIIPHRP 15 824 EALWVEERF 15 5 LTLATEQPV 14 11 QPVKKNTLK 14 18 LKKYKIACI 14 19 KKYKIACIV 14 43 LGLRKLEKQ 14 124 DCCADYKSV 14 158 LPPVILFSM 14 181 MPNINKLKT 14 215 GLYPESHGI 14 258 TAMYQGLKA 14 308 LPKAERPRF 14 347 HAFGMLMEG 14 360 NLHNCVNII 14 398 MYEGPAPRI 14 411 IPHDFFSFN 14 500 GPSFKEKTE 14 507 TEVEPFENI 14 519 NLMCDLLRI 14 537 GSLNHLLKV 14 545 VPFYEPSHA 14 566 NPLPTESLD 14 671 VPPSESQKC 14 672 PPSESQKCS 14 15 KNTLKKYKI 13 39 LGLGLGLRK 13 184 INKLKTCGI 13 198 RAMYPTKTF 13 204 KTFPNHYTI 13 217 YPESHGIID 13 265 KAATYFWPG 13 277 AINGSFPSI 13 329 HAGGPVSAR 13 337 RVIKALQVV 13 359 RNLHNCVNI 13 440 LTPDLPKRL 13 446 KRLHYAKNV 13 468 LAVRSKSNT 13 487 NEFRSMEAI 13 528 QPAPNNGTH 13 529 PAPNNGTHG 13 549 EPSHAEEVS 13 564 FANPLPTES 13 577 CPHLQNSTQ 13 596 TQEEITATV 13 655 SPLPPTVPD 13 757 GHFDAPDEI 13 775 PIPTHYFVV 13 796 NCPGWLDVL 13 807 IIPHRPTNV 13 833 TAHIARVRD 13 850 FYQDKVQPV 13 41 LGLGLRKLE 12 73 VACKDRGDC 12 126 CADYKSVCQ 12 146 TAQQSQCPE 12 152 CPEGFDLPP 12 176 TWDTLMPNI 12 225 DNNMYDVNL 12 271 WPGSEVAIN 12 272 PGSEVAING 12 282 FPSIYMPYN 12 285 IYMPYNGSV 12 361 LHNCVNIIL 12 370 LADHGMDQT 12 390 FPRINFFYM 12 401 GPAPRIRAH 12 402 PAPRIRAHN 12 419 NSEEIVRNL 12 431 KPDQHFKPY 12 441 TPDLPKRLH 12 444 LPKRLHYAK 12 455 RIDKVHLFV 12 509 VEPFENIEV 12 548 YEPSHAEEV 12 592 MLNLTQEEI 12 598 EEITATVKV 12 600 ITATVKVNL 12 636 KAMRMPMWS 12 648 VPQLGDTSP 12 651 LGDTSPLPP 12 666 RADVRVPPS 12 715 VPMYEEFRK 12 723 KMWDYFHSV 12 742 GVNVVSGPI 12 768 HLANTDVPI 12 778 THYFVVLTS 12 811 RPTNVESCP 12 822 KPEALWVEE 12 828 VEERFTAHI 12 834 AHIARVRDV 12 V2-HLA-B5101-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 82; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 5 DCLQRKDCC 6 4 DDCLQRKDC 5 2 CSDDCLQRK 3 3 SDDCLQRKD 3 7 LQRKDCCAD 3 1 SCSDDCLQR 2 V3-HLA-B5101-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 85; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 7 CPGGKPEAL 19 9 GGKPEALWV 16 V4-HLA-B5101-9mers-161P2F10B Each peptide is a portion of SEQ ID NO: 88; each start position is specified, the length of the peptide is 9 amino acids and the end position for each peptide is the start position plus 8. 2 YLPTFETPI 15 1 TYLPTFETP 7

TABLE XXXIV Pos 1234567890 score V1-HLA-A1-10MERS-161P2F10B Each peptide is a portion of SEQ ID NO: 81; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 441 TPDLPKRLHY 32 771 NTDVPIPTHY 31 858 VSEILQLKTY 30 673 PSESQKCSFY 29 718 YEEFRKMWDY 27 370 LADHGMDQTY 25 746 VSGPIFDYNY 24 280 GSFPSIYMPY 23 617 QKNVDHCLLY 23 164 FSMDGFRAEY 21 311 AERPRFYTMY 21 386 MTDYFPRINF 21 388 DYFPRINFFY 20 390 FPRINFFYMY 20 697 ASNRTSDSQY 20 220 SHGIIDNNMY 19 295 FEERISTLLK 19 420 SEEIVRNLSC 19 506 KTEVEPFENI 19 508 EVEPFENIEV 19 737 ATERNGVNVV 19 430 RKPDQHFKPY 18 685 DKNITHGFLY 18 800 WLDVLPFIIP 18 8 ATEQPVKKNT 17 12 PVKKNTLKKY 17 155 GFDLPPVILF 17 166 MDGFRAEYLY 17 187 LKTCGIHSKY 17 192 IHSKYMRAMY 17 201 YPTKTFPNHY 17 208 NHYTIVTGLY 17 277 AINGSFPSIY 17 419 NSEEIVRNLS 17 476 TNCGGGNHGY 17 509 VEPFENIEVY 17 709 LITSNLVPMY 17 841 DVELLTGLDF 17 115 CSDDCLQKKD 16 217 YPESHGIIDN 16 252 GQPMWLTAMY 16 260 MYQGLKAATY 16 539 LNHLLKVPFY 16 569 PTESLDCFCP 16 637 AMRMPMWSSY 16 701 TSDSQYDALI 16 762 PDEITKHLAN 16 842 VELLTGLDFY 16 120 LQKKDCCADY 15 257 LTAMYQGLKA 15 273 GSEVAINGSF 15 308 LPKAERPRFY 15 321 FEEPDSSGHA 15 376 DQTYCNKMEY 15 380 CNKMEYMTDY 15 547 FYEPSHAEEV 15 553 AEEVSKFSVC 15 572 SLDCFCPHLQ 15 621 DHCLLYHREY 15 744 NVVSGPIFDY 15 V2-HLA-A1-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 83; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 3 CSDDCLQRKD 16 8 LQRKDCCADY 15 4 SDDCLQRKDC 13 10 RKDCCADYKS 12 1 CSCSDDCLQR 10 V3-HLA-A1-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 86; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 4 NVESCPGGKP 13 6 ESCPGGKPEA 8 2 PTNVESCPGG 6 9 PGGKPEALWV 6 V4-HLA-A1-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 89; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 1 KTYLPTFETP 9 2 TYLPTFETPI 4

TABLE XXXV Pos 1234567890 score V1-HLA-A0201-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 81; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 28 LLALLVIMSL 30 22 KIACIVLLAL 27 30 ALLVIMSLGL 26 36 SLGLGLGLGL 24 708 ALITSNLVPM 24 835 HIARVRDVEL 24 17 TLKKYKIACI 23 222 GIIDNNMYDV 23 284 SIYMPYNGSV 23 806 FIIPHRPTNV 23 23 IACIVLLALL 22 34 IMSLGLGLGL 22 39 LGLGLGLRKL 22 111 SLCSCSDDCL 22 165 SMDGFRAEYL 22 178 DTLMPNINKL 22 215 GLYPESHGII 22 302 LLKWLDLPKA 22 397 YMYEGPAPRI 22 439 YLTPDLPKRL 22 595 LTQEEITATV 22 615 VLQKNVDHCL 22 25 CIVLLALLVI 21 157 DLPPVILFSM 21 352 LMEGLKQRNL 21 450 YAKNVRIDKV 21 639 RMPMWSSYTV 21 723 KMWDYFHSVL 21 32 LVIMSLGLGL 20 293 VPFEERISTL 20 360 NLHNCVNIIL 20 564 FANPLPTESL 20 591 QMLNLTQEEI 20 737 ATERNGVNVV 20 836 IARVRDVELL 20 4 TLTLATEQPV 19 369 LLADHGMDQT 19 447 RLHYAKNVRI 19 607 NLPFGRPRVL 19 656 PLPPTVPDCL 19 682 YLADKNITHG 19 692 FLYPPASNRT 19 825 ALWVEERFTA 19 26 IVLLALLVIM 18 183 NINKLKTCGI 18 204 KTFPNHYTIV 18 259 AMYQGLKAAT 18 267 ATYFWPGSEV 18 276 VAINGSFPSI 18 329 HAGGPVSARV 18 347 HAFGMLMEGL 18 534 GTHGSLNHLL 18 594 NLTQEEITAT 18 833 TAHIARVRDV 18 27 VLLALLVIMS 17 42 GLGLRKLEKQ 17 162 ILFSMDGFRA 17 175 YTWDTLMPNI 17 180 LMPNINKLKT 17 186 KLKTCGIHSK 17 227 NMYDVNLNKN 17 335 SARVIKALQV 17 361 LHNCVNIILL 17 418 FNSEEIVRNL 17 518 YNLMCDLLRI 17 536 HGSLNHLLKV 17 552 HAEEVSKFSV 17 580 LQNSTQLEQV 17 624 LLYHREYVSG 17 660 TVPDCLRADV 17 736 HATERNGVNV 17 768 HLANTDVPIP 17 775 PIPTHYFVVL 17 861 ILQLKTYLPT 17 6 TLATEQPVKK 16 20 KYKIACIVLL 16 31 LLVIMSLGLG 16 131 SVCQGETSWL 16 152 CPEGFDLPPV 16 196 YMRAMYPTKT 16 230 DVNLNKNFSL 16 269 YFWPGSEVAI 16 336 ARVIKALQVV 16 366 NIILLADHGM 16 374 GMDQTYCNKM 16 467 WLAVRSKSNT 16 526 RIQPAPNNGT 16 599 EITATVKVNL 16 606 VNLPFGRPRV 16 700 RTSDSQYDAL 16 792 HTPENCPGWL 16 839 VRDVELLTGL 16 855 VQPVSEILQL 16 9 TEQPVKKNTL 15 24 ACIVLLALLV 15 171 AEYLYTWDTL 15 224 IDNNMYDVNL 15 257 LTAMYQGLKA 15 333 PVSARVIKAL 15 343 QVVDHAFGML 15 355 GLKQRNLHNC 15 359 RNLHNCVNII 15 454 VRIDKVHLFV 15 460 HLFVDQQWLA 15 461 LFVDQQWLAV 15 491 SMEAIFLAHG 15 496 FLAHGPSFKE 15 519 NLMCDLLRIQ 15 530 APNNGTHGSL 15 538 SLNHLLKVPF 15 541 HLLKVPFYEP 15 583 STQLEQVNQM 15 592 MLNLTQEEIT 15 642 MWSSYTVPQL 15 706 YDALITSNLV 15 731 VLLIKHATER 15 765 ITKHLANTDV 15 774 VPIPTHYFVV 15 817 SCPEGKPEAL 15 827 WVEERFTAHI 15 846 TGLDFYQDKV 15 33 VIMSLGLGLG 14 57 KCFDASFRGL 14 64 RGLENCRCDV 14 65 GLENCRCDVA 14 173 YLYTWDTLMP 14 191 GIHSKYMRAM 14 232 NLNKNFSLSS 14 338 VIKALQVVDH 14 341 ALQVVDHAFG 14 350 GMLMEGLKQR 14 368 ILLADHGMDQ 14 494 AIFLAHGPSF 14 508 EVEPFENIEV 14 533 NGTHGSLNHL 14 547 FYEPSHAEEV 14 584 TQLEQVNQML 14 709 LITSNLVPMY 14 722 RKMWDYFHSV 14 732 LLIKHATERN 14 734 IKHATERNGV 14 773 DVPIPTHYFV 14 830 ERFTAHIARV 14 844 LLTGLDFYQD 14 849 DFYQDKVQPV 14 859 SEILQLKTYL 14 866 TYLPTFETTI 14 V2-HLA-A0201-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 83; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 7 CLQRKDCCAD 11 2 SCSDDCLQRK 7 6 DCLQRKDCCA 5 V3-HLA-A0201-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 86; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 7 SCPGGKPEAL 15 9 PGGKPEALWV 8 V4-HLA-A0201-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 89; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 2 TYLPTFETPI 12 1 KTYLPTFETP 8

TABLE XXXVI Pos 1234567890 score V1-HLA-A0203-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 81; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 258 TAMYQGLKAA 19 259 AMYQGLKAAT 17 15 KNTLKKYKIA 10 21 YKIACIVLLA 10 52 GSCRKKCFDA 10 65 GLENCRCDVA 10 101 FRCGETRLEA 10 118 DCLQKKDCCA 10 138 SWLEENCDTA 10 162 ILFSMDGFRA 10 190 CGIHSKYMRA 10 239 LSSKEQNNPA 10 250 WHGQPMWLTA 10 257 LTAMYQGLKA 10 268 TYFWPGSEVA 10 302 LLKWLDLPKA 10 321 FEEPDSSGHA 10 327 SGHAGGPVSA 10 332 GPVSARVIKA 10 339 IKALQVVDHA 10 362 HNCVNIILLA 10 394 NFFYMYEGPA 10 399 YEGPAPRIRA 10 442 PDLPKRLHYA 10 460 HLFVDQQWLA 10 485 YNNEFRSMEA 10 489 FRSMEAIFLA 10 521 MCDLLRIQPA 10 544 KVPFYEPSHA 10 556 VSKFSVCGFA 10 593 LNLTQEEITA 10 628 REYVSGFGKA 10 658 PPTVPDCLRA 10 675 ESQKCSFYLA 10 688 ITHGFLYPPA 10 699 NRTSDSQYDA 10 728 FHSVLLIKHA 10 752 DYNYDGHFDA 10 761 APDEITKHLA 10 816 ESCPEGKPEA 10 825 ALWVEERFTA 10 828 VEERFTAHIA 10 16 NTLKKYKIAC 9 22 KIACIVLLAL 9 53 SCRKKCFDAS 9 66 LENCRODVAC 9 102 RCGETRLEAS 9 119 CLQKKDCCAD 9 139 WLEENCDTAQ 9 163 LFSMDGFRAE 9 191 GIHSKYMRAM 9 240 SSKEQNNPAW 9 251 HGQPMWLTAM 9 269 YFWPGSEVAI 9 303 LKWLDLPKAE 9 322 EEPDSSGHAG 9 328 GHAGGPVSAR 9 333 PVSARVIKAL 9 340 KALQVVDHAF 9 363 NCVNIILLAD 9 395 FFYMYEGPAP 9 400 EGPAPRIRAH 9 443 DLPKRLHYAK 9 461 LFVDQQWLAV 9 486 NNEFRSMEAI 9 490 RSMEAIFLAH 9 522 CDLLRIQPAP 9 545 VPFYEPSHAE 9 557 SKFSVCGFAN 9 594 NLTQEEITAT 9 629 EYVSGFGKAM 9 659 PTVPOCLRAD 9 676 SQKCSFYLAD 9 689 THGFLYPPAS 9 700 RTSDSQYDAL 9 729 HSVLLIKHAT 9 753 YNYDGHFDAP 9 762 PDEITKHLAN 9 817 SCPEGKPEAL 9 826 LWVEERFTAH 9 829 EERFTAHIAR 9 V2-HLA-A0203-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 83; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 6 DCLQRKDCCA 10 7 CLQRKDCCAD 9 8 LQRKDCCADY 8 V3-HLA-A0203-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 86; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 6 ESCPGGKPEA 10 7 SCPGGKPEAL 9 8 CPGGKPEALW 8 V2-HLA-A0203-10mers-161P2F10B No Results Found.

TABLE XXXVII Pos 1234567890 score V1-HLA-A3-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 81; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 38 GLGLGLGLRK 27 6 TLATEQPVKK 26 186 KLKTCGIHSK 26 301 TLLKWLDLPK 25 337 RVIKALQVVD 25 838 RVRDVELLTG 25 47 KLEKQGSCRK 23 179 TLMPNINKLK 23 256 WLTAMYQGLK 23 277 AINGSFPSIY 23 212 IVTGLYPESH 21 422 EIVRNLSCRK 21 437 KPYLTPDLPK 21 443 DLPKRLHYAK 21 462 FVDQQWLAVR 21 494 AIFLAHGPSF 21 605 KVNLPFGRPR 21 730 SVLLJKHATE 21 731 VLLIKHATER 21 781 FVVLTSCKNK 21 841 DVELLTGLDF 21 195 KYMRAMYPTK 20 368 ILLADHGMDQ 20 495 IFLAHGPSFK 20 624 LLYHREYVSG 20 630 YVSGFGKAMR 20 664 CLRADVRVPP 20 708 ALITSNLVPM 20 714 LVPMYEEFRK 20 26 IVLLALLVIM 19 32 LVIMSLGLGL 19 107 RLEASLCSCS 19 338 VIKALQVVDH 19 523 DLLRIQPAPN 19 538 SLNHLLKVPF 19 588 QVNQMLNLTQ 19 596 TQEEITATVK 19 609 PFGRPRVLQK 19 669 VRVPPSESQK 19 802 DVLPFIIPHR 19 5 LTLATEQPVK 18 30 ALLVIMSLGL 18 36 SLGLGLGLGL 18 160 PVILFSMDGF 18 173 YLYTWDTLMP 18 215 GLYPESHGII 18 260 MYQGLKAATY 18 364 CVNIILLADH 18 426 NLSCRKPDQH 18 447 RLHYAKNVRI 18 453 NVRIDKVHLF 18 697 ASNRTSDSQY 18 825 ALWVEERFTA 18 12 PVKKNTLKKY 17 41 LGLGLRKLEK 17 46 RKLEKQGSCR 17 121 QKKDCCADYK 17 233 LNKNFSLSSK 17 311 AERPRFYTMY 17 405 RIRAHNIPHD 17 458 KVHLFVDQQW 17 469 AVRSKSNTNC 17 524 LLRIQPAPNN 17 544 KVPFYEPSHA 17 637 AMRMPMWSSY 17 650 QLGDTSPLPP 17 670 RVPPSESQKC 17 692 FLYPPASNRT 17 713 NLVPMYEEFR 17 742 GVNVVSGPIF 17 831 RFTAHIARVR 17 22 KIACIVLLAL 16 25 CIVLLALLVI 16 67 ENCRCDVACK 16 113 CSCSDDCLQK 16 284 SIYMPYNGSV 16 295 FEERISTLLK 16 341 ALQVVDHAFG 16 423 IVRNLSCRKP 16 455 RIDKVHLFVD 16 549 EPSHAEEVSK 16 603 TVKVNLPFGR 16 614 RVLQKNVDHC 16 623 CLLYHREYVS 16 744 NVVSGPIFDY 16 758 HFDAPDEITK 16 775 PIPTHYFVVL 16 783 VLTSCKNKSH 16 806 FIIPHRPTNV 16 835 HIARVRDVEL 16 854 KVQPVSEILQ 16 861 ILQLKTYLPT 16 11 QPVKKNTLKK 15 27 VLLALLVIMS 15 28 LLALLVIMSL 15 55 RKKCFDASFR 15 65 GLENCRCDVA 15 131 SVCQGETSWL 15 157 DLPPVILFSM 15 161 VILFSMDGFR 15 162 ILFSMDGFRA 15 223 IIDNNMYDVN 15 232 NLNKNFSLSS 15 285 IYMPYNGSVP 15 307 DLPKAERPRF 15 331 GGPVSARVIK 15 343 QVVDHAFGML 15 367 IILLADHGMD 15 369 LLADHGMDQT 15 516 EVYNLMCDLL 15 526 RIQPAPNNGT 15 607 NLPFGRPRVL 15 660 TVPDCLRADV 15 668 DVRVPPSESQ 15 677 QKCSFYLADK 15 709 LITSNLVPMY 15 764 EITKHLANTD 15 844 LLTGLDFYQD 15 863 QLKTYLPTFE 15 17 TLKKYKIACI 14 263 GLKAATYFWP 14 292 SVPFEERIST 14 305 WLDLPKAERP 14 344 VVDHAFGMLM 14 348 AFGMLMEGLK 14 428 SCRKPDQHFK 14 439 YLTPDLPKRL 14 467 WLAVRSKSNT 14 555 EVSKFSVCGF 14 567 PLPTESLDCF 14 579 HLQNSTQLEQ 14 599 EITATVKVNL 14 619 NVDHCLLYHR 14 656 PLPPTVPDCL 14 807 IIPHRPTNVE 14 827 WVEERFTAHI 14 847 GLDFYQDKVQ 14 857 PVSEILQLKT 14 44 GLRKLEKQGS 13 72 DVACKDRGDC 13 91 ESTRIWMCNK 13 139 WLEENCDTAQ 13 192 IHSKYMRAMY 13 226 NNMYDVNLNK 13 230 DVNLNKNFSL 13 267 ATYFWPGSEV 13 304 KWLDLPKAER 13 330 AGGPVSARVI 13 333 PVSARVIKAL 13 335 SARVIKALQV 13 446 KRLHYAKNVR 13 490 RSMEAIFLAH 13 508 EVEPFENIEV 13 527 IQPAPNNGTH 13 535 THGSLNHLLK 13 560 SVCGFANPLP 13 585 QLEQVNQMLN 13 627 HREYVSGFGK 13 647 TVPQLGDTSP 13 682 YLADKNITHG 13 726 DYFHSVLLIK 13 732 LLIKHATERN 13 749 PIFDYNYDGH 13 779 HYFVVLTSCK 13 834 AHIARVRDVE 13 V2-HLA-A3-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 83; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 9 QRKDCCADYK 17 7 CLQRKDCCAD 14 2 SCSDDCLQRK 12 8 LQRKDCCADY 12 1 CSCSDDCLQR 10 V3-HLA-A3-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 86; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 4 NVESCPGGKP 14 3 TNVESCPGGK 13 10 GGKPEALWVE 8 9 PGGKPEALWV 7 V4-HLA-A3-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 89; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 1 KTYLPTFETP 12 2 TYLPTFETPI 6

TABLE XXXVIII Pos 1234567890 score V1-HLA-A26-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 81; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 555 EVSKFSVCGF 32 178 DTLMPNINKL 29 744 NVVSGPIFDY 29 516 EVYNLMCDLL 28 841 DVELLTGLDF 28 230 DVNLNKNFSL 27 297 ERISTLLKWL 27 12 PVKKNTLKKY 25 343 QVVDHAFGML 25 32 LVIMSLGLGL 24 154 EGFDLPPVIL 23 333 PVSARVIKAL 23 388 DYFPRINFFY 23 599 EITATVKVNL 23 795 ENCPGWLDVL 23 802 DVLPFIIPHR 23 160 PVILFSMDGF 22 453 NVRIDKVHLF 22 508 EVEPFENIEV 22 719 EEFRKMWDYF 22 709 LITSNLVPMY 21 131 SVCQGETSWL 20 275 EVAINGSFPS 20 293 VPFEERISTL 20 488 EFRSMEAIFL 20 853 DKVQPVSEIL 20 72 DVAGKDRGDC 19 105 ETRLEASLCS 19 376 DQTYCNKMEY 19 421 EEIVRNLSCR 19 571 ESLDCFCPHL 19 668 DVRVPPSESQ 19 685 DKNITHGFLY 19 742 GVNVVSGPIF 19 792 HTPENCPGWL 19 22 KIACIVLLAL 18 92 STRIWMCNKF 18 136 ETSWLEENCD 18 312 ERPRFYTMYF 18 422 EIVRNLSCRK 18 494 AIFLAHGPSF 18 513 ENIEVVNLMC 18 587 EQVNQMLNLT 18 598 EEITATVKVN 18 621 DHCLLYHREY 18 659 PTVPDGLRAD 18 700 RISDSQYDAL 18 771 NTDVPIPTHY 18 773 DVPIPTHYFV 18 830 ERFTAHIARV 18 386 MTDYFPRINF 17 457 DKVHLFVDQQ 17 629 EYVSGFGKAM 17 653 DTSPLPPTVP 17 726 DYFHSVLLIK 17 760 DAPDEITKHL 17 838 RVRDVELLTG 17 87 DTCVESTRIW 16 89 CVESTRIWMC 16 145 DTAQQSQGPE 16 210 YTIVTGLYPE 16 296 EERISTLLKW 16 307 DLPKAERPRF 16 510 EPFENIEVYN 16 534 GTHGSLNHLL 16 574 DCFCPHLQNS 16 602 ATVKVNLPFG 16 763 DEITKHLANT 16 764 EITKHLANTD 16 277 AINGSFPSIY 15 280 GSFPSIYMPY 15 400 EGPAPRIRAH 15 493 EAIFLAHGPS 15 554 EEVSKFSVCG 15 646 YTVPQLGDTS 15 739 ERNGVNVVSG 15 820 EGKPEALWVE 15 858 VSEILQLKTY 15 V2-HLA-A26-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 83; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 8 LQRKDCCADY 10 5 DDCLQRKDCC 8 6 DCLQRKDCCA 8 2 SCSDDCLQRK 6 V3-HLA-A26-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 86; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 4 NVESCPGGKP 14 6 ESCPGGKPEA 11 7 SCPGGKPEAL 10 2 PINVESCPGG 8 3 TNVESCPGGK 8 V4-HLA-A26-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 89; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 1 KTYLPTFETP 9

TABLE XXXIX Pos 1234567890 score V1-HLA-B0702-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 81; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 431 KPDQHFKPYL 23 530 APNNGTHGSL 22 648 VPQLGDTSPL 22 577 CPHLQNSTQL 21 797 CPGWLDVLPF 21 152 CPEGFDLPPV 20 293 VPFEERISTL 20 776 IPTHYFVVLT 20 500 GPSFKEKTEV 19 761 APDEITKHLA 19 246 NPAWWHGQPM 18 658 PPTVPDCLRA 18 672 PPSESQKCSF 18 715 VPMYEEFRKM 18 774 VPIPTHYFVV 18 332 GPVSARVIKA 17 804 LPFIIPHRPT 17 22 KIACIVLLAL 15 34 IMSLGLGLGL 15 549 EPSHAEEVSK 15 608 LPFGRPRVLQ 15 11 QPVKKNTLKK 14 30 ALLVIMSLGL 14 313 RPRFYTMYFE 14 333 PVSARVIKAL 14 401 GPAPRIRAHN 14 403 APRIRAHNIP 14 437 KPYLTPDLPK 14 441 TPDLPKRLHY 14 488 EFRSMEAIFL 14 599 EITATVKVNL 14 612 RPRVLQKNVD 14 642 MWSSYYTVPQ 14 700 RTSOSQYDAL 14 775 PIPTHYFVVL 14 836 IARVRDVELL 14 19 KKYKIACIVL 13 20 KYKIACIVLL 13 36 SLGLGLGLGL 13 154 EGFDLPPVIL 13 165 SMDGFRAEYL 13 224 IDNNMYDVNL 13 287 MPYNGSVPFE 13 299 ISTLLKWLDL 13 323 EPDSSGHAGG 13 390 EPRINEFYMY 13 418 FNSEEIVRNL 13 435 HFKPYLTPDL 13 452 KNVRIDKVHL 13 510 EPFENIEVYN 13 528 QPAPNNGTHG 13 566 NPLPTESLDC 13 640 MPMWSSYTVP 13 655 SPLPPTVPDC 13 684 ADKNITHGFL 13 694 YPPASNRTSD 13 705 QYDALITSNL 13 724 MWDYFHSVLL 13 795 ENCPGWLDVL 13 808 IPHRPTNVES 13 818 CPEGKPEALW 13 822 KPEALWVEER 13 835 HIARVRDVEL 13 23 IACIVLLALL 12 32 LVIMSLGLGL 12 39 LGLGLGLRKL 12 57 KCFDASFRGL 12 171 AEYLYTWDTL 12 206 FPNHYTIVTG 12 207 PNHYTIVTGL 12 248 AWWHGQPMWL 12 282 FPSIYMPYNG 12 308 LPKAERPRFY 12 347 HAFGMLMEGL 12 352 LMEGLKQRNL 12 534 GTHGSLNHLL 12 564 FANPLPTESL 12 571 ESLDCFCPHL 12 586 LEQVNQMLNL 12 661 VPDCLRADVR 12 674 SESQKCSFYL 12 695 PPASNRTSDS 12 723 KMWDYFHSVL 12 811 RPTNVESCPE 12 839 VRDVELLTGL 12 855 VQPVSEILQL 12 9 TEQPVKKNTL 11 28 LIALLVIMSL 11 76 KDRGDCCWDF 11 99 NKFRCGETRL 11 101 FRCGETRLEA 11 103 CGETRLEASL 11 131 SVCQGETSWL 11 158 LPPVILFSMD 11 201 YPTKTFPNHY 11 253 QPMWLTAMYQ 11 271 WPGSEVAING 11 294 PFEERISTLL 11 297 ERISTLLKWL 11 325 DSSGHAGGPV 11 330 AGGPVSARVI 11 343 QVVDHAFGML 11 411 IPHDFFSFNS 11 439 YLTPDLPKRL 11 444 LPKRLHYAKN 11 511 PFENIEVYNL 11 515 IEVYNLMCDL 11 516 EVYNLMCDLL 11 545 VPFYEPSHAE 11 555 EVSKFSVCGF 11 559 FSVCGFANPL 11 568 LPTESLDCFC 11 607 NLPFGRPRVL 11 615 VLQKNVDHCL 11 656 PLPPTVPDCL 11 688 ITHGFLYPPA 11 708 ALITSNLVPM 11 760 DAPDEITKHL 11 767 KHLANTDVPI 11 817 SCPEGKPEAL 11 859 SEILQLKTYL 11 V2-HLA-B0702-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 83; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 6 DCLQRKDCCA 6 8 LQRKDCCADY 4 1 CSCSDDCLQR 2 2 SCSDDCLQRK 2 4 SDDCLQRKDC 2 10 RKDCCADYKS 2 3 CSDDCLQRKD 1 7 CLQRKDCCAD 1 V3-HLA-B0702-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 86; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 8 CPGGKPEALW 14 7 SCPGGKPEAL 13 1 RPTNVESCPG 12 9 PGGKPEALWV 10 6 ESCPGGKPEA 9 V4-HLA-B0702-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 89; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 2 TYLPTFETPI 9

TABLE XL Pos 1234567890 score V1-HLA-B08-10mers-161P2F10B No Results Found. V2-HLA-B08-10mers-161P2F10B No Results Found. V3-HLA-B08-10mers-161P2F10B No Results Found. V4-HLA-B08-10mers-161P2F10B No Results Found.

TABLE XLI Pos 1234567890 score V1-HLA-B1510-10mers-161P2F10B No Results Found. V2-HLA-B1510-10mers-161P2F10B No Results Found. V3-HLA-B1510-10mers-161P2F10B No Results Found. V4-HLA-B1510-10mers-161P2F10B No Results Found.

TABLE XLII Pos 1234567890 score V1-HLA-B2705-10mers-161P2F10B No Results Found. V2-HLA-B2705-10mers-161P2F10B No Results Found. V3-HLA-B2705-10mers-161P2F10B No Results Found. V4-HLA-B2705-10mers-161P2F10B No Results Found.

TABLE XLIII Pos 1234567890 score V1-HLA-B2709-10mers-161P2F10B No Results Found. V2-HLA-B2709-10mers-161P2F10B No Results Found. V3-HLA-B2709-10mers-161P2F10B No Results Found. V4-HLA-B2709-10mers-161P2F10B No Results Found.

TABLE XLIV Pos 1234567890 score V1-HLA-B4402-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 81; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 311 AERPRFYTMY 26 9 TEQPVKKNTL 25 171 AEYLYTWDTL 25 296 EERISTLLKW 25 509 VEPFENIEVY 25 719 EEFRKMWDYF 25 859 SEILQLKTYL 25 487 NEFRSMEAIF 24 842 VELLTGLDFY 23 674 SESQKCSFYL 22 586 LEQVNQMLNL 21 823 PEALWVEERF 21 153 PEGFDLPPVI 20 515 IEVYNLMCDL 20 598 EEITATVKVN 20 718 YEEFRKMWDY 20 297 ERISTLLKWL 18 333 PVSARVIKAL 18 154 EGFDLPPVIL 17 322 EEPDSSGHAG 17 330 AGGPVSARVI 17 409 HNIPHDFFSF 17 795 ENCPGWLDVL 17 20 KYKIACIVLL 16 57 KCFDASFRGL 16 178 DTLMPNINKL 16 293 VPFEERISTL 16 421 EEIVRNLSCR 16 439 YLTPDLPKRL 16 494 AIFLAHGPSF 16 855 VQPVSEILQL 16 22 KIACIVLLAL 15 30 ALLVIMSLGL 15 39 LGLGLGLRKL 15 155 GFDLPPVILF 15 277 AINGSFPSIY 15 280 GSFPSIYMPY 15 312 ERPRFYTMYF 15 340 KALQWVVHAF 15 361 LHNCVNIILL 15 388 DYFPRINFFY 15 399 YEGPAPRIRA 15 430 RKPDQHFKPY 15 553 AEEVSKFSVC 15 607 NLPFGRPRVL 15 656 PLPPTVPDCL 15 697 ASNRTSDSQY 15 760 DAPDEITKHL 15 763 DEITKHLANT 15 772 TDVPIPTHYF 15 775 PIPTHYFVVL 15 817 SCPEGKPEAL 15 829 EERFTAHIAR 15 1 MESTLTLATE 14 12 PVKKNTLKKY 14 28 LLALLVIMSL 14 32 LVIMSLGLGL 14 74 ACKDRGDCCW 14 99 NKFRCGETRL 14 141 EENCDTAQQS 14 147 AQQSQCPEGF 14 160 PVILFSMDGF 14 165 SMDGFRAEYL 14 197 MRAMYPTKTF 14 208 NHYTIVTGLY 14 218 PESHGIIDNN 14 248 AWWHGQPMWL 14 269 YFWPGSEVAI 14 295 FEERISTLLK 14 353 MEGLKQRNLH 14 387 TDYFPRINFF 14 435 HFKPYLTPDL 14 441 TPDLPKRLHY 14 453 NVRIDKVHLF 14 488 EFRSMEAIFL 14 516 EVVNLMCDLL 14 530 APNNGTHGSL 14 555 EVSKFSVCGF 14 564 FANPLPTESL 14 571 ESLDCFCPHL 14 684 ADKNITHGFL 14 700 RTSDSQYDAL 14 744 NVVSGPIFDY 14 791 SHTPENCPGW 14 858 VSEILQLKTY 14 19 KKYKIACIVL 13 34 IMSLGLGLGL 13 36 SLGLGLGLGL 13 50 KQGSGRKKCF 13 66 LENCRCDVAC 13 85 FEDTCVESTR 13 92 STRIWMCNKF 13 104 GETRLEASLC 13 140 LEENCDTAQQ 13 164 FSMDGFRAEY 13 228 MYDVNLNKNF 13 240 SSKEQNNPAW 13 242 KEQNNPAWWH 13 260 MYQGLKPATY 13 276 VAINGSFPSI 13 321 FEEPDSSGHA 13 347 HAFGMLMEGL 13 360 NLHNCVNIIL 13 381 NKMEYMTDYF 13 384 EYMTDYFPRI 13 386 MTDYFPRINF 13 418 FNSEEIVRNL 13 452 KNVRIDKVHL 13 458 KVHLFVDQQW 13 533 NGTHGSLNHL 13 534 GTHGSLNHLL 13 554 EEVSKFSVCG 13 567 PLPTESLDCF 13 570 TESLDCFCPH 13 597 QEEITATVKV 13 599 EITATVKVNL 13 637 AMRMPMWSSY 13 642 MWSSYTVPQL 13 683 LADKNITHGF 13 716 PMYEEFRKMW 13 723 KMWDYFHSVL 13 724 MWDYFHSVLL 13 738 TERNGVNVVS 13 746 VSGPIFDYNY 13 771 NTDVPIPTHY 13 815 VESCPEGKPE 13 828 VEERETAHIA 13 862 LQLKTYLPTF 13 866 TYLPTFETTI 13 23 IACIVLLALL 12 25 CIVLLALLVI 12 48 LEKQGSCRKK 12 76 KDRGDCCWDF 12 87 DTCVESTRIW 12 90 VESTRIWMCN 12 131 SVCQGETSWL 12 168 GFRAEYLYTW 12 192 IHSKYMRAMY 12 201 YPTKTFPNHY 12 220 SHGIIDNNMY 12 224 IDNNMYOVNL 12 241 SKEQNNPAWW 12 252 GQPMWLTAMY 12 255 MWLTAMYQGL 12 261 YQGLKPATYF 12 262 QGLKAATYFW 12 286 YMPYNGSVPF 12 299 ISTLLKWLDL 12 307 DLPKAERPRF 12 308 LPKAERPRFY 12 343 QVVDHAFGML 12 352 LMEGLKQRNL 12 370 LADHGMDQTY 12 402 PAPRIRAHNI 12 406 IRAHNIPHDF 12 420 SEEIVRNLSC 12 431 KPDQHFKPYL 12 476 TNCGGGNHGY 12 492 MEAIFLAHGP 12 504 KEKTEVEPFE 12 511 PFENIEVYNL 12 512 FENIEVYNLM 12 538 SLNHLLKVPF 12 539 LNHLLKVPFY 12 548 YEPSHAEEVS 12 550 PSHAEEVSKF 12 559 FSVCGFANPL 12 577 CPHLQNSTQL 12 616 LQKNVDHCLL 12 617 QKNVDHCLLY 12 621 DHCLLYHREY 12 625 LYHREYVSGF 12 628 REYVSGFGKA 12 648 VPQLGDTSPL 12 679 CSFYLADKNI 12 705 QYDALITSNL 12 712 SNLVPMYEEF 12 792 HTPENCPGWL 12 797 CPGWLDVLPF 12 818 CPEGKPEALW 12 819 PEGKPEALWV 12 835 HIARVRDVEL 12 836 IARVRDVELL 12 839 VRDVELLTGL 12 841 DVELLTGLDF 12 V2-HLA-B4402-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 83; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 8 LQRKDCCADY 10 4 SDDCLQRKDC 5 2 SCSDDCLQRK 4 3 CSDDCLQRKD 4 V3-HLA-B4402-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 86; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 7 SCPGGKPEAL 16 5 VESCPGGKPE 13 8 CPGGKPEALW 12 V4-HLA-B4402-10mers-161P2F10B Each peptide is a portion of SEQ ID NO: 89; each start position is specified, the length of the peptide is 10 amino acids and the end position for each peptide is the start position plus 9. 2 TYLPTFETPI 12

TABLE XLV Pos 1234567890 score V1-HLA-B5101-10mers-161P2F10B No Results Found. V2-HLA-B5101-10mers-161P2F10B No Results Found. V3-HLA-B5101-10mers-161P2F10B No Results Found. V4-HLA-B5101-10mers-161P2F10B No Results Found.

TABLE XLVI Pos 123456789012345 score V1-DRB1-0101-15mers-161P2F10B Each peptide is a position of SEQ ID NO: 81; each start position is specified, the length of the peptide is 15 amino acids and the end position for each peptide is the start position plus 14. 207 PNHYTIVTGLYPESH 36 181 MPNINKLKTCGIHSK 35 486 NNEFRSMEAIFLAHG 35 839 VRDVELLTGLDFYQD 33 703 DSQYDALITSNLVPM 32 42 GLGLRKLEKQGSCRK 31 740 RNGVNVVSGPIFDYN 31 28 LLALLVIMSLGLGLG 30 160 PVILFSMDGFRAEYL 30 797 CPGWLDVLPFIIPHR 30 858 VSEILQLKVYLPTFE 30 801 LDVLPFIIPHRPTNV 29 393 INFFYMYEGPAPRIR 28 421 EEIVRNLSCRKPDQH 28 627 HREYVSGFGKAMRMP 28 30 ALLVIMSLGLGLGLG 27 32 LVIMSLGLGLGLGLR 27 34 IMSLGLGLGLGLRKL 27 364 CVNIILLADHGMDQT 27 522 CDLLRIQPAPNNGTH 27 23 IACIVLLALLVIMSL 26 258 TAMYQGLKAATYFWP 26 273 GSEVAINGSFPSIYM 26 283 PSIYMPYNGSVPFEE 26 300 STLLKWLDLPKAERP 26 545 VPFYEPSHAEEVSKF 26 645 SYTVPQLGDTSPLPP 26 778 THYFVVLTSCKNKSH 26 26 IVLLALLVIMSLGLG 25 230 DVNLNKNFSLSSKEQ 25 266 AATYFWPGSEVAING 25 292 SVPFEERISTLLKWL 25 303 LKWLDLPKAERPRFY 25 350 GMLMEGLKQRNLHNC 25 433 DQHFKPYLTPDLPKR 25 459 VHLFVDQQWLAVRSK 25 492 MEAIFLAHGPSFKEK 25 509 VEPFENIEVYNLMCD 25 536 HGSLNHLLKVPFYEP 25 561 VCGFANPLPTESLDC 25 22 KIACIVLLALLVIMS 24 25 CIVLLALLVIMSLGL 24 163 LFSMDGFRAEYLYTW 24 174 LYTWDTLMPNINKLK 24 194 SKYMRAMYPTKTFPN 24 246 NPAWWHGQPMWLTAM 24 313 RPRFYTMYFEEPDSS 24 316 FYTMYFEEPDSSGHA 24 333 PVSARVIKALQVVDH 24 342 LQVVDHAFGMLMEGL 24 387 TDYFPRINFFYMYEG 24 392 RINFFYMYEGPAPRI 24 395 FFYMYEGPAPRIRAH 24 412 PHDFFSFNSEEIVRN 24 437 KPYLTPDLPKRLHYA 24 514 NIEVYNLMCDLLRIQ 24 518 YNLMCDLLRIQPAPN 24 539 LNHLLKVPFYEPSHA 24 542 LLKVPFYEPSHAEEV 24 589 VNQMLNLTQEEITAT 24 605 KVNLPFGRPRVLQKN 24 722 RKMWDYFHSVLLIKH 24 798 PGWLDVLPFIIPHRP 24 45 LRKLEKQGSCRKKCF 23 84 DFEDTCVESTRIWMC 23 129 YKSVCQGETSWLEEN 23 191 GIHSKYMRAMYPTKT 23 210 YTIVTGLYPESHGII 23 272 PGSEVAINGSFPSIY 23 284 SIYMPYNGSVPFEER 23 328 GHAGGPVSARVIKAL 23 464 DQQWLAVRSKSNTNC 23 562 CGFANPLPTESLDCF 23 637 AMRMPMWSSYTVPQL 23 644 SSYTVPQLGDTSPLP 23 651 LGDTSPLPPTVPDCL 23 687 NITHGFLYPPASNRT 23 804 LPFIIPHRPTNVESC 23 1 MESTLTLATEQPVKK 22 18 LKKYKIACIVLLALL 22 20 KYKIACIVLLALLVI 22 145 DTAQQSQCPEGFDLP 22 152 CPEGFDLPPVILFSM 22 155 GFDLPPVILFSMDGF 22 171 AEYLYTWDTLMPNIN 22 380 CNKMEYMTDYFPRIN 22 400 EGPAPRIRAHNIPHD 22 434 QHFKPYLTPDLPKRL 22 575 CFCPHLQNSTQLEQV 22 648 VPQLGDTSPLPPTVP 22 654 TSPLPPTVPDCLRAD 22 777 PTHYFVVLTSCKNKS 22 825 ALWVEERFTAHIARV 22 833 TAHIARVRDVELLTG 22 60 DASFRGLENCRCDVA 21 142 ENCDTAQQSQCPEGF 21 186 KLKTCGIHSKYMRAM 21 451 AKNVRIDKVHLFVDQ 21 490 RSMEAIFLAHGPSFK 21 665 LRADVRVPPSESQKC 21 704 SQYDALITSNLVPMY 21 739 ERNGVNVVSGPIFDY 21 770 ANTDVPIPTHYFVVL 21 98 CNKFRCGETRLEASL 20 253 QPMWLTAMYQGLKAA 20 443 DLPKRLHYAKNVRID 20 521 MCDLLRIQPAPNNGT 20 553 AEEVSKFSVCGFANP 20 623 CLLYHREYVSGFGKA 20 631 VSGFGKAMRMPMWSS 20 718 YEEFRKMWDYFHSVL 20 729 HSVLLIKHATERNGV 20 750 IFDYNYDGHFDAPDE 20 829 EERFTAHIARVRDVE 20 15 KNTLKKYKIACIVLL 19 37 LGLGLGLGLRKLEKQ 19 153 PEGFDLPPVILFSMD 19 158 LPPVILFSMDGFRAE 19 170 RAEYLYTWDTLMPNI 19 226 NNMYDVNLNKNFSLS 19 305 WLDLPKAERPRFYTM 19 340 KALQVVDHAFGMLME 19 346 DHAFGMLMEGLKQRN 19 363 NCVNIILLADHGMDQ 19 413 HDFFSFNSEEIVRNL 19 500 GPSFKEKTEVEPFEN 19 556 VSKFSVCGFANPLPT 19 603 TVKVNLPFGRPRVLQ 19 691 GFLYPPASNRTSDSQ 19 762 PDEITKHLANTDVPI 19 771 NTDVPIPTHYFVVLT 19 817 SCPEGKPEALWVEER 19 2 ESTLTLATEQPVKKN 18 12 PVKKNTLKKYKIACI 18 29 LALLVIMSLGLGLGL 18 102 RCGETRLEASLCSCS 18 136 ETSWLEENCDTAQQS 18 157 DLPPVILFSMDGFRA 18 183 NINKLKTCGIHSKYM 18 214 TGLYPESHGIIDNNM 18 228 MYDVNLNKNFSLSSK 18 255 MWLTAMYQGLKAATY 18 259 AMYQGLKAATYFWPG 18 267 ATYFWPGSEVAINGS 18 297 ERISTLLKWLDLPKA 18 302 LLKWLDLPKAERPRF 18 318 TMYFEEPDSSGHAGG 18 322 EEPDSSGHAGGPVSA 18 362 HNCVNIILLADHGMD 18 382 KMEYMTDYFPRINFF 18 515 IEVYNLMCDLLRIQP 18 595 LTQEEITATVKVNLP 18 613 PRVLQKNVDHCLLYH 18 640 MPMWSSYTVPQLGDT 18 662 PDCLRADVRVPPSES 18 681 FYLADKNITHGFLYP 18 689 THGFLYPPASNRTSD 18 748 GPIFDYNYDGHFDAP 18 847 GLDFYQDKVQPVSEI 18 848 LDFYQDKVQPVSEIL 18 16 NTLKKYKIACIVLLA 17 21 YKIACIVLLALLVIM 17 24 ACIVLLALLVIMSLG 17 31 LLVIMSLGLGLGLGL 17 36 SLGLGLGLGLRKLEK 17 80 DCCWDFEDTCVESTR 17 103 CGETRLEASLCSCSD 17 126 CADYKSVCQGETSWL 17 139 WLEENCDTAQQSQCP 17 147 AQQSQCPEGFDLPPV 17 189 TCGIHSKYMRAMYPT 17 209 HYTIVTGLYPESHGI 17 212 IVTGLYPESHGIIDN 17 227 NMYDVNLNKNFSLSS 17 236 NFSLSSKEQNNPAWW 17 261 YQGLKAATYFWPGSE 17 265 KAATYFWPGSEVAIN 17 282 FPSIYMPYNGSVPFE 17 286 YMPYNGSVPFEERIS 17 324 PDSSGHAGGPVSARV 17 331 GGPVSARVIKALQVV 17 336 ARVIKALQVVDHAFG 17 341 ALQVVDHAFGMLMEG 17 347 HAFGMLMEGLKQRNL 17 372 DHGMDQTYCNKMEYM 17 394 NFFYMYEGPAPRIRA 17 396 FYMYEGPAPRIRAHN 17 491 SMEAIFLAHGPSFKE 17 493 EAIFLAHGPSFKEKT 17 506 KTEVEPFENIEVYNL 17 519 NLMCDLLRIQPAPNN 17 527 IQPAPNNGTHGSLNH 17 540 NHLLKVPFYEPSHAE 17 557 SKFSVCGFANPLPTE 17 597 QEEITATVKVNLPFG 17 601 TATVKVNLPFGRPRV 17 602 ATVKVNLPFGRPRVL 17 629 EYVSGFGKAMRMPMW 17 677 QKCSFYLADKNITHG 17 685 DKNITHGFLYPPASN 17 725 WDYFHSVLLIKHATE 17 726 DYFHSVLLIKHATER 17 734 IKHATERNGVNVVSG 17 780 YFVVLTSCKNKSHTP 17 812 PTNVESCPEGKPEAL 17 823 PEALWVEERFTAHIA 17 836 IARVRDVELLTGLDF 17 842 VELLTGLDFYQDKVQ 17 V2-DRB1-0101-15mers-161P2F10B Each peptide is a position of SEQ ID NO: 84; each start position is specified, the length of the peptide is 15 amino acids and the end position for each peptide is the start position plus 14. 2 EASLCSCSDDCLQRK 16 7 SCSDDCLQRKDCCAD 9 12 CLQRKDCCADYKSVC 9 13 LQRKDCCADYKSVCQ 9 14 QRKDCCADYKSVCQG 9 9 SDDCLQRKDCCADYK 8 10 DDCLQRKDCCADYKS 8 8 CSDDCLQRKDCCADY 7 V3-HLA-DRB1-0101-15mers-161P2F10B Each peptide is a position of SEQ ID NO: 87; each start position is specified, the length of the peptide is 15 amino acids and the end position for each peptide is the start position plus 14. 7 PTNVESCPGGKPEAL 25 12 SCPGGKPEALWVEER 19 4 PHRPTNVESCPGGKP 14 10 VESCPGGKPEALWVE 14 V4-HLA-DRB1-0101-15mers-161P2F10B Each peptide is a position of SEQ ID NO: 90; each start position is specified, the length of the peptide is 15 amino acids and the end position for each peptide is the start position plus 14. 2 ILQLKTYLPTFETPI 16 1 EILQLKTYLPTFETP 10

TABLE XLVII Pos 123456789012345 score V1-HLA-DRB1-0301-15mers-161P2F10B Each peptide is a position of SEQ ID NO: 81; each start position is specified, the length of the peptide is 15 amino acids and the end position for each peptide is the start position plus 14. 437 KPYLTPDLPKRLHYA 31 451 AKNVRIDKVHLFVDQ 31 662 PDCLRADVRVPPSES 28 458 KVHLFVDQQWLAVRS 27 597 QEEITATVKVNLPFG 27 228 MYDVNLNKNFSLSSK 26 350 GMLMEGLKQRNLHNC 26 536 HGSLNHLLKVPFYEP 26 305 WLDLPKAERPRFYTM 25 358 QRNLHNCVNIILLAD 24 30 ALLVIMSLGLGLGLG 22 366 NIILLADHGMDQTYD 22 28 LLALLVIMSLGLGLG 21 32 LVIMSLGLGLGLGLR 21 34 IMSLGLGLGLGLRKL 21 158 LPPVILFSMDGFRAE 21 161 VILFSMDGFRAEYLY 21 517 VYNLMCDLLRIQPAP 21 707 DALITSNLVPMYEEF 21 742 GVNVVSGPIFDYNYD 21 10 EQPVKKNTLKKYKIA 20 20 KYKIACIVLLALLVI 20 109 EASLCSCSDDCLQKK 20 118 DCLQKKDCCADYKSV 20 236 NFSLSSKEQNNPAWW 20 284 SIYMPYNGSVPFEER 20 408 AHNIPHDFFSFNSEE 20 467 WLAVRSKSNTNCGGG 20 615 VLQKNVDHCLLYHRE 20 635 GKAMRMPMWSSYTVP 20 780 YFVVLTSCKNKSHTP 20 839 VRDVELLTGLDFYQD 20 847 GLDFYQDKVQPVSEI 20 855 VQPVSEILQLKTYLP 20 2 ESTLTLATEQPVKKN 19 26 IVLLALLVIMSLGLG 19 38 GLGLGLGLRKLEKQG 19 42 GLGLRKLEKQGSCRK 19 74 ACKDRGDCCWDFEDT 19 129 YKSVCQGETSWLEEN 19 153 PEGFDLPPVILFSMD 19 257 LTAMYQGLKAATYFW 19 331 GGPVSARVIKALQVV 19 335 SARVIKALQVVDHAF 19 341 ALQVVDHAFGMLMEG 19 349 FGMLMEGLKQRNLHN 19 433 DQHFKPYLTPDLPKR 19 486 NNEFRSMEAIFLAHG 19 492 MEAIFIAHGPSFKEK 19 514 NIEVYNLMCDLLRIQ 19 524 LLRIQPAPNNGTHGS 19 553 AEEVSKFSVCGFANP 19 565 ANPLPTESLDCFCPH 19 654 TSPLPPTVPDCLRAD 19 679 CSFYLADKNITHGFL 19 697 ASNRTSDSQYDALIT 19 740 RNGVNVVSGPIFDYN 19 773 DVPIPTHYFVVLTSC 19 781 FVVLTSCKNKSHTPE 19 812 PTNVFSCPEGKPEAL 19 833 TAHIARVRDVELLTG 19 835 HIARVRDVELLTGLD 19 852 QDKVQPVSEILQLKT 19 163 LFSMDGFRAEYLYTW 18 177 WDTLMPNINKLKTCG 18 178 DTLMPNINKLKTCGI 18 224 IDNNMYDVNLNKNFS 18 254 PMWLTAMYQGLKAAT 18 267 ATYFWPGSEVAINGS 18 275 EVAINGSFPSIYMPY 18 292 SVPFEERISTLLKWL 18 296 EERISTLLKWLDLPK 18 445 PKRLHYAKNVRIDKV 18 465 QQWLAVRSKSNTNCG 18 506 KTEVEPFENIEVYNL 18 509 VEPFENIEVYNLMCD 18 582 NSTQLEQVNQMLNLT 18 586 LEQVNQMLNLTQEEI 18 589 VNQMLNLTQEEITAT 18 605 KVNLPFGRPRVLQKN 18 613 PRVLQKNVDHCLLYH 18 621 DHCLLYHREYVSGFG 18 628 REYVSGFGKAMRMPM 18 658 PPTVPDCLRADVRVP 18 711 TSNLVPMYEEFRKMW 18 712 SNLVPMYEEFRKMWD 18 721 FRKMWDYFHSVLLIK 18 731 VLLIKHATERNGVNV 18 7 LATEQPVKKNTLKKY 17 92 STRIWMCNKFRCGET 17 219 ESHGIIDNNMYDVNL 17 282 FPSIYMPYNGSVPFE 17 290 NGSVPFEERISTLLK 17 439 YLTPDLPKRLHYAKN 17 457 DKVHLFVDQQWLAVR 17 500 GPSFKEKTEVEPFEN 17 518 YNLMCDLLRIQPAPN 17 558 KFSVCGFANPLPTES 17 573 LDCFCPHLQNSTQLE 17 577 CPHLQNSTQLEQVNQ 17 583 STQLEQVNQMLNLTQ 17 590 NQMLNLTQEEITATV 17 714 LVPMYEEFRKMWDYF 17 746 VSGPIFDYNYDGHFD 17 823 PEALWVEERFTAHIA 17 857 PVSEILQLKTYLPTF 17 60 DASFRGLENCRCDVA 16 70 RCDVACKDRGDCCWD 16 78 RGDCCWDFEDTCVES 16 94 RIWMCNKFRCGETRL 16 101 FRCGETRLEASLCSC 16 122 KKDCCADYKSVCQGE 16 226 NNMYDVNLNKNFSLS 16 234 NKNFSLSSKEQNNPA 16 346 DHAFGMLMEGLKQRN 16 384 EYMTDYFPRINFFYM 16 450 YAKNVRIDKVHLFVD 16 532 NNGTHGSLNHLLKVP 16 599 EITATVKVNLPFGRP 16 678 KCSFYLADKNITHGF 16 748 GPIFDYNYDGHFDAP 16 24 ACIVLLALLVIMSLG 15 48 LEKQGSCRKKCFDAS 15 56 KKCFDASFRGLENCR 15 97 MCNKFRCGETRLEAS 15 162 ILFSMDGFRAEYLYT 15 164 FSMDGFRAEYLYTWD 15 190 CGIHSKYMRAMYPTK 15 218 PESHGIIDNNMYDVN 15 374 GMDQTYCNKMEYMTD 15 386 MTDYFPRINFFYMYE 15 413 HDFFSFNSEEIVRNL 15 474 SNTNCGGGNHGYNNE 15 478 CGGGNHGYNNEFRSM 15 485 YNNEFRSMEAIFLAH 15 670 RVPPSESQKCSFYLA 15 728 FHSVLLIKHATERNG 15 803 VLPFIIPHRPTNVES 15 821 GKPEALWVEERFTAH 15 V2-DRB1-0301-15mers-161P2F10B Each peptide is a position of SEQ ID NO: 84; each start position is specified, the length of the peptide is 15 amino acids and the end position for each peptide is the start position plus 14. 2 EASLCSCSDDCLQRK 20 11 DCLQRKDCCADYKSV 20 15 RKDCCADYKSVCQGE 16 4 SLCSCSDDCLQRKDC 12 5 LCSCSDDCLQRKDCC 11 10 DDCLQRKDCCADYKS 11 V3-HLA-DRB1-0301-15mers-161P2F10B Each peptide is a position of SEQ ID NO: 87; each start position is specified, the length of the peptide is 15 amino acids and the end position for each peptide is the start position plus 14. 7 PTNVESCPGGKPEAL 13 10 VESCPGGKPEALWVE 10 11 ESCPGGKPEALWVEE 9 9 NVESCPGGKPEALWV 8 1 FIIPHRPTNVESCPG 7 3 IPHRPTNVESCPGGK 6 V4-HLA-DRB1-0301-15mers-161P2F10B Each peptide is a position of SEQ ID NO: 90; each start position is specified, the length of the peptide is 15 amino acids and the end position for each peptide is the start position plus 14. 2 ILQLKTYLPTFETPIJ 12 1 EILQLKTYLPTFETPJ 10

TABLE XLVIII Pos 123456789012345 score V1-HLA-DRB1-0401-15mers-161P2F10B Each peptide is a position of SEQ ID NO: 81; each start position is specified, the length of the peptide is 15 amino acids and the end position for each peptide is the start position plus 14. 126 CADYKSVCQGETSWL 28 412 PHDFFSFNSEEIVRN 28 464 DQQWLAVRSKSNTNC 28 631 VSGFGKAMRMPMWSS 28 691 GFLYPPASNRTSDSQ 28 703 DSQYDALITSNLVPM 28 722 RKMWDYFHSVLLIKH 28 750 IFDYNYDGHFDAPDE 28 777 PTHYFVVLTSCKNKS 28 778 THYFVVLTSCKNKSH 28 28 LLALLVIMSLGLGLG 26 181 MPNINKLKVCGIHSK 26 213 VTGLYPESHGIIDNN 26 290 NGSVPFEERISTLLK 26 350 GMLMEGLKQRNLHNC 26 445 PKRLHYAKNVRIDKV 26 458 KVHLFVDQQWLAVRS 26 506 KTEVEPFENIEVYNL 26 524 LLRIQPAPNNGTHGS 26 583 STQLEQVNQMLNLTQ 26 589 VNQMLNLTQEEITAT 26 823 PEALWVEERFTAHIA 26 855 VQPVSEILQLKYLP 26 18 LKKYKIACIVLLALL 22 60 DASFRGLENCRCDVA 22 80 DCCWDFEDTCVESTR 22 136 ETSWLEENCDTAQQS 22 172 EYLYTWDTLMPNINK 22 174 LYTWDTLMPNINKLK 22 193 HSKYMRAMYPTKTFP 22 203 TKVFPNHYTIVTGLY 22 253 QPMWLTAMYQGLKAA 22 266 AATYFWPGSEVAING 22 279 NGSFPSIYMPYNGSV 22 346 DHAFGMLMEGLKQRN 22 382 KMEYMTDYFPRINFF 22 387 TDYFPRINFFYMYEG 22 415 FFSFNSEEIVRNLSC 22 433 DQHFKPYLTPDLPKR 22 447 RLHYAKNVRIDKVHL 22 482 NHGYNNEFRSMEAIF 22 509 VEPFENIEVYNLMCD 22 573 LDCFCPHLQNSTQLE 22 678 KCSFYLADKNITHGF 22 679 CSFYLADKNITHGFL 22 797 CPGWLDVLPFIIPHR 22 803 VLPFIIPHRPTNVES 22 847 GLDFYQDKVQPVSEI 22 2 ESTLTLATEQPVKKN 20 4 TLTLATEQPVKKNTL 20 20 KYKIACIVLLALLVI 20 23 IACIVLLALLVIMSL 20 24 ACIVLLALLVIMSLG 20 25 CIVLLALLVIMSLGL 20 26 IVLLALLVIMSLGLG 20 42 GLGLRKLEKQGSCRK 20 45 LRKLEKQGSCRKKCF 20 129 YKSVCQGETSWLEEN 20 155 GFDLPPVILFSMDGF 20 163 LFSMDGFRAEYLYTW 20 177 WDTLMPNINKLKTCG 20 178 DTLMPNINKLKTCGI 20 197 MRAMYPTKTFPNHYT 20 225 DNNMYDVNLNKNFSL 20 228 MYDVNLNKNFSLSSK 20 230 DVNLNKNFSLSSKEQ 20 254 PMWLTAMYQGLKAAT 20 273 GSEVAINGSFPSIYM 20 282 FPSIYMPYNGSVPFE 20 300 STLLKWLDLPKAERP 20 305 WLDLPKAERPRFYTM 20 316 FYTMYFEEPDSSGHA 20 335 SARVIKALQWDHAF 20 339 IKALQVVDHAFGMLM 20 342 LQVVDHAFGMLMEGL 20 358 QRNLHNCVNIILLAD 20 364 CVNIILLADHGMDQT 20 365 VNIILLADHGMDQTY 20 366 NIILLADHGMDQTYC 20 408 AHNIPHDFFSFNSEE 20 420 SEEIVRNLSCRKPDQ 20 437 KPYLTPDLPKRLHYA 20 514 NIEVYNLMCDLLRIQ 20 517 VYNLMCDLLRIQPAP 20 518 YNLMCDLLRQPAPN 20 521 MCDLLRIQPAPNNGT 20 558 KFSVCGFANPLPTES 20 570 TESLDGFCPHLQNST 20 577 CPHLQNSTQLEQVNQ 20 586 LEQVNQMLNLTQEEI 20 592 MLNLTQEEITATVKV 20 637 AMRMPMWSSYTVPQL 20 639 RMPMWSSYTVPQLGD 20 658 PPTVPDCLRADVRVP 20 662 PDCLRADVRVPPSES 20 666 RADVRVPPSESQKCS 20 690 HGFLYPPASNRTSDS 20 714 LVPMYEEFRKMWDYF 20 721 FRKMWDYFHSVLLIK 20 728 FHSVLLIKHATERNG 20 730 SVLLIKHATERNGVN 20 771 NTDVPIPTHYFWLT 20 833 TAHIARVRDVELLTG 20 852 QDKVQPVSEILQLKT 20 858 VSEILQLKTYLPTFE 20 84 DFEDTCVESTRIWMC 18 99 NKFRCGETRLEASLC 18 103 CGETRLEASLCSCSD 18 135 GETSWLEENCDTAQQ 18 168 GFRAEYLYTWDTLMP 18 186 KLKTCGIHSKYMRAM 18 200 MYPTKTFPNHYTIVT 18 224 IDNNMYDVNLNKNFS 18 233 LNKNFSLSSKEQNNP 18 237 FSLSSKEQNNPAWWH 18 276 VAINGSFPSIYMPYN 18 293 VPFEERISTLLKWLD 18 319 MYFEEPDSSGHAGGP 18 355 GLKQRNLHNCVNIIL 18 370 LADHGMDQTYCNKME 18 397 YMYEGPAPRIRAHNI 18 409 HNIPHDFFSFNSEEI 18 417 SFNSEEIVRNLSCRK 18 457 DKVHLFVDQQWLAVR 18 463 VDQQWLAVRSKSNTN 18 483 HGYNNEFRSMEAIFL 18 491 SMEAIFLAHGPSFKE 18 533 NGTHGSLNHLLKVPF 18 549 EPSHAEEVSKFSVCG 18 562 CGFANPLPTESLDCF 18 547 DCFCPHLQNSTQLEQ 18 580 LQNSTQLEQVNQMLN 18 593 LNLTQEEITATVKVN 18 604 VKVNLPFGRPRVLQK 18 609 PFGRPRVLQKNVDHC 18 614 RVLQKNVDHCLLYHR 18 669 VRVPPSESQKCSFYL 18 682 YLADKNITHGFLYPP 18 697 ASNRTSDSQYDALIT 18 704 SQYDALITSNLVPMY 18 733 LIKHATERNGVNVVS 18 739 ERNGVNVVSGPIFDY 18 758 HFDAPDEITKHLANT 18 763 DEITKHLANTDVPIP 18 802 DVLPFIIPHRPTNVE 18 844 LLTGLDFYQDKVQPV 18 292 SVPFEERISTLLKWL 17 848 LDFYQDKVQPVSEIL 17 56 KKCFDASFRGLENCR 16 82 CWDFEDTCVESTRIW 16 98 CNKFRCGETRLEASL 16 161 VILFSMDGFRAEYLY 16 166 MDGFRAEYLYTWDTL 16 170 RAEYLYTWDTLMPNI 16 207 PNHYTIVTGLYPESH 16 226 NNMYDVNLNKNFSLS 16 234 NKNFSLSSKEQNNPA 16 246 NPAWWHGQPMQLTAM 16 247 PAWWHGQPMQLTAMY 16 258 TAMYQGLKAATYFWP 16 267 ATYFWPGSEVAINGS 16 268 TYFWPGSEVAINGSF 16 302 LLKWLDLPKAERPRF 16 317 YTMYFEEPDSSGHAG 16 318 TMYFEEPDSSGHAGG 16 392 RINFFYMYEGPAPRI 16 394 NFFYMYEGPAPRIRA 16 413 HDFFSFNSEEIVRNL 16 459 VHLFVDQQWLAVRSK 16 486 NNEFRSMEAIFLAHG 16 493 EAIFLAHGPSFKEKT 16 544 KVPFYEPSHAEEVSK 16 545 VPFYEPSHAEEVSKF 16 561 VCGFANPLPTESLDC 16 607 NLPFGRPRVLQKNVD 16 623 CLLYHREYVSGFGKA 16 627 HREYVSGFGKAMRMP 16 640 MPMWSSYTVPQLGDT 16 643 WSSYTVPQLGDTSPL 16 715 VPMYEEFRKMWDYFH 16 724 MWDYFHSVLLIKHAT 16 725 WDYFHSVLLIKHATE 16 756 DGHFDAPDEITKHLA 16 824 EALWVEERFTAHIAR 16 441 TPDLPKRLHYAKNVR 15 825 ALWVEERFTAHIARV 15 15 KNTLKKYKIACIVLL 14 30 ALLVIMSLGLGLGLG 14 31 LLVIMSLGLGLGLGL 14 32 LVIMSLGLGLGLGLR 14 34 IMSLGLGLGLGLRKL 14 36 SLGLGLGLGLRKLEK 14 38 GLGLGLGLRKLEKQG 14 63 FRGLENCRCDVACKD 14 105 ETRKEASKCSCSDDC 14 109 EASLCSCSDDCKQKK 14 137 TSWLEENCDTAQQSQ 14 158 LPPVILFSMDGFRAE 14 160 PVILFSMDGFRAEYL 14 171 AEYLYTWDTLMPNIN 14 184 INKLKTCGIHSKYMR 14 194 SKYMRAMYPTKTFPN 14 209 HYTIVTGLYPESHGI 14 210 YTIVTGLYPESHGII 14 220 SHGIIDNNMYDVNLN 14 221 HGIIDNNMYDVNLNK 14 257 LTAMYQGLKAATYFW 14 261 YQGLKAATYFWPGSE 14 284 SIYMPYNGSVPFEER 14 296 EERISTLLKWLDLPK 14 299 ISTLLKWLDLPKAER 14 336 ARVIKALQVVDHAFG 14 341 ALQVVDHAFGMLMEG 14 348 AFGMLMEGLKQRNLH 14 349 FGMLMEGLKQRNLHN 14 362 HNCVNIILLADHGMD 14 367 IILLADHGMDQTYCN 14 372 DHGMDQTYCNKMEYM 14 383 MEYMTDYFPRINFFY 14 390 FPRINFFYMYEGPAP 14 395 FFYMYEGPAPRIRAH 14 421 EEIVRNLSCRKPDQH 14 451 AKNVRIDKVHLFVDQ 14 453 NVRIDKVHLFVDQQW 14 456 IDKVHLFVDQQWLAV 14 489 FRSMEAIFLAHGPSF 14 492 MEAIFLAHGPSFKEK 14 494 AIFLAHGPSFKEKTE 14 522 CDLLRIQPAPNNGTH 14 536 HGSLNHLLKVPFYEP 14 539 LNHLLKVPFYEPSHA 14 540 NHLLKVPFYEPSHAE 14 542 LLKVPFYEPSHAEEV 14 553 AEEVSKFSVCGFANP 14 565 ANPLPTESLDCFCPH 14 590 NQMLNLTQEEITATV 14 597 QEEITATVKVNLPFG 14 605 KVNLPFGRPRVLQKN 14 613 PRVLQKNVDHCLLYH 14 621 DHCLLYHREYVSGFG 14 628 REYVSGFGKAMRMPM 14 645 SYTVPQLGDTSPLPP 14 654 TSPLPPTVPDCLRAD 14 668 DVRVPPSESQKCSFY 14 706 YDALITSNLVPMYEE 14 712 SNLVPMYEEFRKMWD 14 731 VLLIKHATERNGVNV 14 740 RNGVNVVSGPIFDYN 14 743 VNVVSGPIFDYNYDG 14 773 DVPIPTHYFVVLTSC 14 778 HYFVVLTSCKNKSHT 14 780 YFVVLTSCKNKSHTP 14 781 FVVLTSCKNKSHTPE 14 798 PGWLDVLPFIIPHRP 14 800 WLDVLPFIIPHRPTN 14 801 LDVLPFIIPHRPTNV 14 804 LPFIIPHRPTNVESC 14 836 IARVRDVELLTGLDF 14 839 VRDVELLTGLDFYQD 14 841 DVELLTGLDFYQDKV 14 842 VELLTGLDFYQDKVQ 14 845 LTGLDFYQDKVQPVS 14 V2-HLA-DR1-0401-15mers-161P2F10B Each peptide is a position of SEQ ID NO: 84; each start position is specified, the length of the peptide is 15 amino acids and the end position for each peptide is the start position plus 14. 2 EASLCSCSDDCLQRK 14 5 LCSCSDDCLQRKDCC 12 7 SCSDDCKQRKDCCAD 12 14 QRKDCCADYKSVCQG 12 1 LEASLCSCSDDCLQR 6 3 ASLCSCSDDCLQRKD 6 4 SLCSCSDDCLQRKDC 6 6 CSCSDDCLQRKDCCA 6 11 DCLQRKDCCADYKSV 6 12 CLQRKDCCADYKSVC 6 13 LQRKDCCADYKSVCQ 6 15 RJDCCADYKSVCQGE 6 V3-HLA-DR1-0401-15mers-161P2F10B Each peptide is a position of SEQ ID NO: 87; each start position is specified, the length of the peptide is 15 amino acids and the end position for each peptide is the start position plus 14. 1 FIIPHRPTNVESCPG 12 4 PHRPTNVESCPGGKP 12 7 PTNVESCPGGKPEAL 8 5 HRPTNVESCPGGKPE 6 6 RPTNVESCPGGKPEA 6 9 NVESCPGGKPEALWV 6 10 VESCPGGKPEALWVE 6 12 SCPGGKPEALWVEER 6 13 CPGGKPEALWVEERF 6 14 PGGKPEALWVEERFT 6 15 GGKPEALWVEERFTA 6 V4-HLA-DR1-0401-15mers-161P2F10B Each peptide is a position of SEQ ID NO: 90; each start position is specified, the length of the peptide is 15 amino acids and the end position for each peptide is the start position plus 14. 2 ILQLKTYLPTFETPI 8

TABLE XLIX Pos 123456789012345 score V1-HLA-DRB1-1101-15mers-161P2F10B Each peptide is a portion of SEQ ID NO: 81; each start position is specified, the length of the peptide is 15 amino acids and the end position for each peptide is the start position plus 14. 339 IKALQVVDHAFGMLM 27 42 GLGLRKLEKQGSCRK 26 518 YNLMCDLLRIQPAPN 26 207 PNHYTIVTGLYPESH 24 302 LLKWLDLPKAERPRF 24 750 IFDYNYDGHFDAPDE 24 392 RINFFYMYEGPAPRI 23 417 SFNSEEIVRNLSCRK 23 313 RPRFYTMYFEEPDSS 22 662 PDCLRAOVRVPPSES 22 160 PVILFSMDGFRAEYL 21 178 DTLMPNINKLKTCGI 21 296 EERISTLLKWLDLPK 21 759 FDAPDEITKHLANTD 21 780 YFVVIJSCKNKSHTP 21 823 PEALWVEERFTAHIA 21 227 NMYDVNLNKNFSLSS 20 421 EEIVRNLSGRKPDQH 20 447 RLHYAKNVRIDKVHL 20 491 SMEAIFLAHGPSFKE 20 536 HGSLNHLLKVPFYEP 20 728 FHSVLLIKHATERNG 20 798 PGWLDVLPFIIPHRP 20 801 LDVLPFIIPHRPTNV 20 29 LALLVIMSLGLGLGL 19 31 LLVIMSLGLGLGLGL 19 56 KKCFDASFRGLENCR 19 300 STLLKWLDLPKAERP 19 678 KCSFYLADKNITHGF 19 848 LDFYQOKVQPVSEIL 19 858 VSEILQLKTYLPTFE 19 25 CIVLLALLVIMSLGL 18 60 DASFRGLENCRCDVA 18 234 NKNFSLSSKEQNNPA 18 266 AATYFWPGSEVAING 18 380 CNKMEYMTDYFPRIN 18 482 NHGYNNEFRSMEAIF 18 489 FRSMEAIFLAHGPSF 18 539 LNHLLKVPFYEPSHA 18 544 KVPFYEPSHAEEVSK 18 597 QEEITATVKVNLPFG 18 631 VSGFGKAMRMPMWSS 18 645 SYTVPQLGDTSPLPP 18 715 VPMYEEFRKMWDYFH 18 777 PTHYFVVLTSCKNKS 18 778 THYFVVLTSCKNKSH 18 803 VLPFIIPHRPTNVES 18 836 IARVRDVELLTGLDF 18 68 NCRCDVACKDRGDCC 17 93 TRIWMCNKFRCGETR 17 174 LYTWDTLMPNINKLK 17 283 PSIYMPYNGSVPFEE 17 317 YTMYFEEPDSSGHAG 17 346 DHAFGMLMEGLKQRN 17 463 VDQQWLAVRSKSNTN 17 515 IEVYNLMCDLLRIQP 17 441 TPDLPKRLHYAKNVR 14 450 YAKNVRIDKVHLFVD 14 550 PSHAEEVSKFSVCGF 14 602 ATVKVNLPFGRPRVL 14 628 REYVSGFGKAMRMPM 14 658 PPTVPDCLPADVRVP 14 682 YLADKNITHGFLYPP 14 685 DKNITHGFLYPPASN 14 714 LVPMYEEFRKMWDYF 14 724 MWDYFHSVLLIKHAT 14 727 YFHSVLLIKHATERN 14 740 RNGVNVVSGPIFDYN 14 771 NTDVPIPTHYFVVLT 14 814 NVESCPEGKPEALVN 14 829 EERFTAHIARVRDVE 14 842 VELLTGLDFYQDKVQ 14 23 IACIVLLALLVIMSL 13 27 VLLALLVIMSLGLGL 13 28 LLALLVIMSLGLGLG 13 33 VIMSLGLGLGLGLRK 13 63 FRGLENCRCDVACKD 13 194 SKYMRAMYPTKTFPN 13 225 DNNMYDVNLNKNFSL 13 350 GMLMEGLKQRNLHNC 13 434 QHFKPYLTPDLPKRL 13 453 NVRIDKVHLFVDQQW 13 514 NIEVYNLMCDLLRIQ 13 540 NHLLKVPFYEPSHAE 13 558 KFSVGGFANPLPTES 13 583 STQLEQVNQMLNLTQ 13 598 EEITATVKVNLPFGR 13 621 DHCLLYHREYVSGFG 13 643 WSSYTVPQLGDTSPL 13 651 LGDTSPLPPTVPDCL 13 726 DYFHSVLLIKHATER 13 731 VLLIKHATERNGVNV 13 766 TKHLANTDVPIPTHY 13 812 PTNVESCPEGKPEAL 13 852 QDKVQPVSEILQLKT 13 855 VQPVSEILQLKTYLP 13 556 VSKFSVCGFANPLPT 17 691 GFLYPPASNRTSDSQ 17 725 WDYFHSVLLIKHATE 17 797 CPGWLDVLPFIIPHR 17 92 STRIWMCNKFRCGET 16 126 CADYKSVCQGETSWL 16 136 ETSWLEENCOTAQQS 16 258 TAMYQGLKAATYFWP 16 279 NGSFPSIYMPYNGSV 16 305 WLDLPKAERPRFYTM 16 349 FGMLMEGLKQRNLHN 16 387 TDYFPRINFFYMYEG 16 393 INFFYMYEGPAPRIR 16 397 YMYEGPAPRIRAHNI 16 438 PYLTPDLPKRLHYAK 16 464 DQQWLAVRSKSNTNC 16 486 NNEFRSMEAIFLAHG 16 500 GPSFKEKTEVEPFEN 16 509 VEPFENIEVYNLMCD 16 561 VCGFANPLPTESLDC 16 610 FGRPRVLQKNVDHCL 16 703 DSQYDALITSNLVPM 16 718 YEEFRKMWDYFHSVL 16 802 DVLPFIIPHRPTNVE 16 830 ERFTAHIARVRDVEL 16 12 PVKKNTLKKYKIACI 15 38 GLGLGLGLRKLEKQG 15 213 VTGLYPESHGIIDNN 15 254 PMWLTAMYQGLKAAT 15 332 GPVSARVIKALQVVD 15 401 GPAPRIRAHNIPHDF 15 427 LSCRKPDQHFKPYLT 15 458 KVHLFVDQQWLAVRS 15 465 QQWLAVRSKSNTNCG 15 533 NGTHGSLNHLLKVPF 15 614 RVLQKNVDHCLLYHR 15 619 NVDHCLLYHREYVSG 15 721 FRKMWDYFHSVLLIK 15 846 TGLDFYQOKVQPVSE 15 7 LATEQPVKKNTLKKY 14 20 KYKIACIVLLALLVI 14 26 IVLLALLVIMSLGLG 14 39 LGLGLGLRKLEKQGS 14 70 RCDVACKDRGDCCWD 14 94 RIWMCNKFRCGETRL 14 99 NKFRCGETRLEASLC 14 114 SCSDDCLQKKDCCAD 14 180 LMPNINKLKTCGIHS 14 196 YMRAMYPTKTFPNHY 14 210 YTIVTGLYPESHGII 14 243 EQNNPAWWHGQPMWL 14 257 LTAMYQGLKAATYFW 14 290 NGSVPFEERISTLLK 14 303 LKWLDLPKAERPRFY 14 321 FEEPDSSGHAGGPVS 14 365 VNIILLADHGMDQTY 14 405 RIRAHNIPHDFFSFN 14 441 TPDLPKRLHYAKNVR 14 450 YAKNVRIDKVHLFVD 14 550 PSHAEEVSKFSVCGF 14 602 ATVKVNLPFGRPRVL 14 628 REYVSGFGKAMRMPM 14 658 PPTVPDCLRADVRVP 14 682 YLADKNITHGFLYPP 14 685 DKNITHGFLYPPASN 14 714 LVPMYEEFRKMWDYF 14 724 MWDYFHSVLLIKHAT 14 727 YFHSVLLIKHATERN 14 740 RNGVNVVSGPIFDYN 14 771 NTDVPIPTHYFVVLT 14 814 NVESCPEGKPEALWV 14 829 EERFTAHIARVRDVE 14 842 VELLTGLDFYQDKVQ 14 23 IACIVLLALLVIMSL 13 27 VLLALLVIMSLGLGL 13 28 LLALLVIMSLGLGLG 13 33 VIMSLGLGLGLGLRK 13 63 FRGLENCRCDVACKD 13 194 SKYMRAMYPTKTFPN 13 225 DNNMYDVNLNKNFSL 13 350 GMLMEGLKQRNLHNC 13 434 QHFKPYLTPDLPKRL 13 453 NVRIDKVHLFVDQQW 13 514 NIEVYNLMCDLLRIQ 13 540 NHLLKVPFYEPSHAE 13 558 KFSVCGFANPLPTES 13 583 STQLEQVNQMLNLTQ 13 598 EEITATVKVNLPFGR 13 621 DHCLLYHREYVSGFG 13 643 WSSYTVPQLGDTSPL 13 651 LGDTSPLPPTVPDCL 13 726 DYFHSVLLIKHATER 13 731 VLLIKHATERNGVNV 13 766 TKHLANTDVPIPTHY 13 812 PTNVESCPEGKPEAL 13 852 QDKVQPVSEILQLKT 13 855 VQPVSEILQLKTYLP 13 V2-DRB1-1101-15mers-161P2F10B Each peptide is a portion of SEQ ID NO: 84; each start position is specified, the length of the peptide is 15 amino acids and the end position for each peptide is the start position plus 14. 7 SCSDDCLQRKOCCAD 14 15 RKDCCADYKSVCQGE 9 8 CSDDCLQRKDCCADY 8 13 LQRKDCCADYKSVCQ 7 2 EASLCSCSDDCLQRK 6 9 SDDCLQRKDCCADYK 6 10 DDCLQRKDCCADYKS 6 V3-HLA-DRB1-1101-15mers-161P2F10B Each peptide is a portion of SEQ ID NO: 87; each start position is specified, the length of the peptide is 15 amino acids and the end position for each peptide is the start position plus 14. 4 PHRPTNVESCPGGKP 14 9 NVESCPGGKPEALWV 14 7 PTNVESCPGGKPEAL 13 3 IPHRPTNVESCPGGK 8 5 HRPTNVESCPGGKPE 7 1 FIIPHRPTNVESCPG 6 15 GGKPEALWVEERFTA 6 V4-HLA-DRB1-1101-15mers-161P2F10B Each peptide is a portion of SEQ ID NO: 90; each start position is specified, the length of the peptide is 15 amino acids and the end position for each peptide is the start position plus 14. 2 ILQLKTYLPTFETPI 6

TABLE L Properties of 161P2F10B Bioinformatic Program Outcome Feature Bioinformatic Outcome Program ORF (includes stop codon) ORF finder # of amino acids 875 Transmembrane region TM Pred One TM, aa 23–41 HMMTop One TM, aa 23–45 Sosui One TM, aa 23–45 TMHMM One TM, aa 23–45 Signal Peptide Signal P None pI pI/MW tool 6.12 Molecular weight pI/MW tool 100.09 kDa Localization PSORT Plasma membrane 74% Golgi 30% PSORT II Endoplasmic 30.4% Golgi 21.7% Motifs Pfam Somatomedin B, Type I phosphodiesterase/ nucleotide pyrophosphatase Prints Cell Attachement RGD Blocks Somatomedin B, DNA/RNA non-specific endonuclease, Prosite Somatomedin B

TABLE LI Nucleotide sequence of transcript variant 161P2F10B v.6 (SEQ ID NO: 91) atacagtttc tctttgccag actagactaa agaaggagca ctactttatt ctgataaaac 60 aggtctatgc agctaccagg acaatggaat ctacgttgac tttagcaacg gaacaacctg 120 ttaagaagaa cactcttaag aaatataaaa tagcttgcat tgttcttctt gctttgctgg 180 tgatcatgtc acttggatta ggcctggggc ttggactcag gaaactggaa aagcaagyca 240 gctgcaggaa gaagtgcttt gatgcatcat ttagaggact ggagaactgc cggtgtgatg 300 tggcatgtaa agaccgaggt gattgctgct gggattttga agacacctgt gtggaatcaa 360 ctcgaatatg gatqtgcaat aaatttcgtt gtggagagac cagattagag gccagccttt 420 gctcttgttc agatgactgt ttgcagagga aagattgctg tgctgactat aagagtgttt 480 gccaaggaga aacctcatgg ctggaagaaa actgtgacac agcccagcag tctcagtgcc 540 cagaaggytt tgacctgcca ccagttatct tgttttctat ggatggattt agagccgaat 600 atttatacac atgygatact ttaatgccaa atatcaataa actgaaaaca tgtggaattc 660 attcaaaata catyagagct atgtatccta ccaaaacctt cccaaatcat tacaccattg 720 tcacgggctt gtatccggag tcacatggca tcattgacaa taatatgtat gatgtaaatc 780 tcaacaagaa tttttcactt tcttcaaagg aacaaaataa tccagcctgg tggcatgggc 840 aaccaatgtg gctgacagca atgtatcaag gtttaaaagc cgctacctac ttttggcccg 900 gatcagaagt ggctataaat ggctcctttc cttccatata catgccttac aacggaagtg 960 tcccatttga agagaggatt tctacactgt taaaatggct ggacctgccc aaagctgaga 1020 gacccaggtt ttataccaty ttttttgaag aacctgattc ctctggacat gcaggtggac 1080 cagtcagtgc cagagtaatt aaagccttac aggtagtaga tcatgctttt gggatgttga 1140 tggaaggcct gaagcagcgg aatttgcaca actgtgtcaa tatcatcctt ctggctgacc 1200 atggaatgga ccagacttat tgtaacaaga tggaatacat gactgattat tttcccagaa 1260 taaacttctt ctacatgtac gaagggcctg ccccccgcgt ccgagctcat aatatacctc 1320 atgacttttt tagttttaat tctgaggaaa ttgttagaaa cctcagttgc cgaaaacctg 1380 atcagcattt caagccctat ttgactcctg atttgccaaa gcgactgcac tatgccaaga 1440 acgtcagaat cgacaaagtt catctctttg tggatcaaca gtggctggct gttaggagta 1500 aatcaaatac aaattgtgga gyaggcaacc atgyttataa caatgagttt aggagcatgg 1560 aggctatctt tctggcacat ggacccagtt ttaaagagaa gactgaagtt gaaccatttg 1620 aaaatattga agtctataac ctaatgtgtg atcttctacg cattcaacca gcaccaaaca 1680 atggaaccca tggtagttta aaccatcttc tgaaggtgcc tttttatgag ccatcccatg 1740 cagaggaggt gtcaaagttt tctgtttgtg gctttgctaa tccattgccc acagagtctc 1800 ttgactgttt ctgccctcac ctacaaaata gtactcagct ggaacaagtg aatcagatgc 1860 taaatctcac ccaagaagaa ataacagcaa cagtgaaagt aaatttgcca tttgggaggc 1920 ctagggtact gcagaagaac gtggaccact gtctccttta ccacagggaa tatgtcagtg 1980 gatttggaaa agctatgagg atgcccatgt ggagttcata cacagtcccc cagttgggag 2040 acacatcgcc tctgcctccc actgtcccag actgtctgcg ggctgatgtc agggttcctc 2100 cttctgagag ccaaaaatgt tccttctatt tagcagacaa gaatatcacc cacqgcttcc 2160 tctatcctcc tgccagcaat agaacatcag atagccaata tgatgcttta attactagca 2220 atttggtacc tatgtatgaa gaattcagaa aaatgtggga ctacttccac agtgttcttc 2280 ttataaaaca tgccacagaa agaaatggag taaatgtggt tagtggacca atatttgatt 2340 ataattatga tggccatttt gatgctccag atgaaattac caaacattta gccaacactg 2400 atgttcccat cccaacacac tactttgtgg tgctgaccag ttgtaaaaac aagagccaca 2460 caccggaaaa ctgccctggg tggctggatg tcctaccctt tatcatccct caccgaccta 2520 ccaacgtgga gagctgtcct gaaggtaaac cagaagctct ttgggttgaa gaaagattta 2580 cagctcacat tgcccgggtc cgtgatgtag aacttctcac tgggcttgac ttctatcagg 2640 ataaagtgca gcctgtctct gaaattttgc aactaaagac atatttacca acatttgaaa 2700 ccactattta acttaataat gtctacttaa tatataattt actgtataaa gtaattttgg 2760 caaaatataa gtgatttttt tctggagaat tgtaaaataa agttttctat ttttccttaa 2820 gtcccctaaa agccataatt tttattattc ctttttctct tttttcaatt ctatgaatat 2880 gtattatttt aaagttatat ttttcacaca gagatgatgc tatattacac cttccctttt 2940 ttgttggttt cttaaactct aatctcatga cagattatac cttccttatt acttgtttta 3000 tcttactcag aatctttgaa tatatttttc tgcccagaat tatctaaaca aaagggagaa 3060 caaaagaagt atgtctcact tgggaactga atcaactcta aatcagtttt gtcacaaaac 3120 tttttgtatt tgactggcaa tgctgattaa aattaaaaat gcaca 3165

TABLE LII Nucleotide sequence alignment of 161P2F10B v.1 (SEQ ID NO: 92) and 161P2F10B v.6 (SEQ ID NO: 93) Score = 5301 bits (2757), Expect 0.0Identities = 2774/2780 (99%), Gaps = 1/2780 (0%) Strand = Plus/Plus

TABLE LIII Peptide sequences of protein coded by 161p2f10b V.6 (SEQ ID NO: 94) MESTLTLATE QPVKKNTLKK YKIACIVLLA LLVIMSLGLG LGLGLRKLEK QGSCRKKCFD 60 ASFRGLENCR CDVACKDRGD CCWDFEDTCV ESTRIWMCNK FRCGETRLEA SLCSCSDDCL 120 QKKDCCADYK SVCQGETSWL EENCDTAQQS ACPEGFDLPP VILFSMDGFR AEYLYTWDTL 180 MPNINKLKTC GIHSKYMRAM YPTKTFPNHY TIVTGLYPES HGIIDNNMYD VNLNKNFSLS 240 SKEQNNPAWW HGQPMWLTAM YQGLKAATYF WPGSEVAING SFPSIYMPYN GSVPFEERIS 300 TLLKWLDLPK AERPRFYTMY FEEPDSSGHA GGPVSARVIK ALQVVDHAFG MLMEGLKQRN 360 LHNCVNIILL ADHGMDQTYC NKMEYMTDYF PRINFFYMYE GPAPRIRAHN IPHDFFSFNS 420 EEIVRNLSCR KPDQHFKPYL TPDLPKRLHY AKNVRIDKVH LFVDQQWLAV RSKSNTNCGG 480 GNHGYNNEFR SMEAIFLAHG PSFKEKTEVE PFENIEVYNL MCDLLRIQPA PNNGTHGSLN 540 HLLKVPFYEP SHAEEVSKFS VCGFANPLPT ESLDCFCPHL QNSTQLEQVN QMLNLTQEEI 600 TATVKVNLPF GRPRVLQKNV DHCLLYHREY VSGFGKAMRM PMWSSYTVPQ LGDTSPLPPT 660 VPDCLRADVR VPPSESQKCS FYLADKNITH GFLYPPASNR TSDSQYDALI TSNLVPMYEE 720 FRKMWDYFHS VLLIKHATER NGVNVVSGPI FDYNYDGHFD APDEITKHLA NTDVPIPTHY 780 FVVLTSCKNK SHTPENCPGW LDVLPFIIPH RPTNVESCPE GKPEALWVEE RFTAHIARVR 840 DVELLTGLDF YQDKVQPVSE ILQLKTYLPT FETTI 875

TABLE LIV Amino acid sequence alignment of 161P2F10Bv.1 v.1 (SEQ ID NO: 95) and 161P2F10B v.6 (SEQ ID NO: 96) Score = 1855 bits (4804),    Expect = 0.0    Identities = 875/875 (100%), Positives = 875/875 (100%) 161P2F10Bv.1: 1 MESTLTLATEQPVKKNTLKKYKIACIVLLALLVIMSLGLGLGLGLRKLEKQGSCRKKCFD 60 MESTLTLATEQPVKKNTLKKYKIACIVLLALLVIMSLGLGLGLGLRKLEKQGSCRKKCFD 161P2F10Bv.6: 1 MESTLTLATEQPVKKNTLKKYKIACIVLLALLVIMSLGLGLGLGLRKLEKQGSCRKKCFD 60 161P2F10Bv.1: 61 ASFRGLENCRCDVACKDRGDCCWDFEDTCVESTRIWMCNKFRCGETRLEASLCSCSDDCL 120 ASFRGLENCRCDVACKDRGDCCWDFEDTCVESTRIWMCNKFRCGETRLEASLCSCSDDCL 161P2F10Bv.6: 61 ASFRGLENCRCDVACKDRGDCCWDFEDTCVESTRIWMCNKFRCGETRLEASLCSCSDDCL 120 161P2F10Bv.1: 121 QKKDCCADYKSVCQGETSWLEENCDTAQQSQCPEGFDLPPVILFSMDGFRAEYLYTWDTL 180 QKKDCCADYKSVCQGETSWLEENCDTAQQSQCPEGFDLPPVILFSMDGFRAEYLYTWDTL 161P2F10Bv.6: 121 QKKDCCADYKSVCQGETSWLEENCDTAQQSQCPEGFDLPPVILFSMDGFRAEYLYTWDTL 180 161P2F10Bv.1: 181 MPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVTGLYPESHGIIDNNMYDVNLNKNFSLS 240 MPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVTGLYPESHGIIDNNMYDVNLNKNFSLS 161P2F10Bv.6: 181 MPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVTGLYPESHGIIDNNMYDVNLNKNFSLS 240 161P2F10Bv.1: 241 SKEQNNPAWWHGQPMWLTAMYQGLKAATYFWPGSEVAINGSFPSIYMPYNGSVPFEERIS 300 SKEQNNPAWWHGQPMWLTAMYQGLKAATYFWPGSEVAINGSFPSIYMPYNGSVPFEERIS 161P2F10Bv.6: 241 SKEQNNPAWWHGQPMWLTAMYQGLKAATYFWPGSEVAINGSFPSIYMPYNGSVPFEERIS 300 161P2F10Bv.1: 301 TLLKWLDLPKAERPRFYTMYFEEPDSSGHAGGPVSARVIKALQVVDHAFGMLMEGLKQRN 360 TLLKWLDLPKAERPRFYTMYFEEPDSSGHAGGPVSARVIKALQVVDHAFGMLMEGLKQRN 161P2F10Bv.6: 301 TLLKWLDLPKAERPRFYTMYFEEPDSSGHAGGPVSARVIKALQVVDHAFGMLMEGLKQRN 360 161P2F10Bv.1: 361 LHNCVNIILLADHGMDQTYCNKMEYMTDYFPRINFFYMYEGPAPRIRAHNIPHDFFSFNS 420 LHNCVNIILLADHGMDQTYCNKMEYMTDYFPRINFFYMYEGPAPRIRAHNIPHDFFSFNS 161P2F10Bv.6: 361 LHNCVNIILLADHGMDQTYCNKMEYMTDYFPRINFFYMYEGPAPRIRAHNIPHDFFSFNS 420 161P2F10Bv.1: 421 EEIVRNLSCRKPDQHFKPYLTPDLPKRLHYAKNVRIDKVHLFVDQQWLAVRSKSNTNCGG 480 EEIVRNLSCRKPDQHFKPYLTPDLPKRLHYAKNVRIDKVHLFVDQQWLAVRSKSNTNCGG 161P2F10Bv.6: 421 EEIVRNLSCRKPDQHFKPYLTPDLPKRLHYAKNVRIDKVHLFVDQQWLAVRSKSNTNCGG 480 161P2F10Bv.1: 481 GNHGYNNEFRSMEAIFLAHGPSFKEKTEVEPFENIEVYNLMCDLLRIQPAPNNGTHGSLN 540 GNHGYNNEFRSMEAIFLAHGPSFKEKTEVEPFENIEVYNLMCDLLRIQPAPNNGTHGSLN 161P2F10Bv.6: 481 GNHGYNNEFRSMEAIFLAHGPSFKEKTEVEPFENIEVYNLMCDLLRIQPAPNNGTHGSLN 540 161P2F10Bv.1: 541 HLLKVPFYEPSHAEEVSKFSVCGFANPLPTESLDCFCPHLQNSTQLEQVNQMLNLTQEEI 600 HLLKVPFYEPSHAEEVSKFSVCGFANPLPTESLDCFCPHLQNSTQLEQVNQMLNLTQEEI 161P2F10Bv.6: 541 HLLKVPFYEPSHAEEVSKFSVCGFANPLPTESLDCFCPHLQNSTQLEQVNQMLNLTQEEI 600 161P2F10Bv.1: 601 TATVKVNLPFGRPRVLQKNVDHCLLYHREYVSGFGKAMRMPMWSSYTVPQLGDTSPLPPT 660 TATVKVNLPFGRPRVLQKNVDHCLLYHREYVSGFGKAMRMPMWSSYTVPQLGDTSPLPPT 161P2F10Bv.6: 601 TATVKVNLPFGRPRVLQKNVDHCLLYHREYVSGFGKAMRMPMWSSYTVPQLGDTSPLPPT 660 161P2F10Bv.1: 661 VPDCLRADVRVPPSESQKCSFYLADKNITHGFLYPPASNRTSDSQYDALITSNLVPMYEE 720 VPDCLRADVRVPPSESQKCSFYLADKNITHGFLYPPASNRTSDSQYDALITSNLVPMYEE 161P2F10Bv.6: 661 VPDCLRADVRVPPSESQKCSFYLADKNITHGFLYPPASNRTSDSQYDALITSNLVPMYEE 720 161P2F10Bv.1: 721 FRKMWDYFHSVLLIKHATERNGVNVVSGPIFDYNYDGHFDAPDEITKHLANTDVPIPTHY 780 FRKMWDYFHSVLLIKHATERNGVNVVSGPIFDYNYDGHFDAPDEITKHLANTDVPIPTHY 161P2F10Bv.6: 721 FRKMWDYFHSVLLIKHATERNGVNVVSGPIFDYNYDGHFDAPDEITKHLANTDVPIPTHY 780 161P2F10Bv.1: 781 FVVLTSCKNKSHTPENCPGWLDVLPFIIPHRPTNVESCPEGKPEALWVEERFTAHIARVR 840 FVVLTSCKNKSHTPENCPGWLDVLPFIIPHRPTNVESCPEGKPEALWVEERFTAHIARVR 161P2F10Bv.6: 781 FVVLTSCKNKSHTPENCPGWLDVLPFIIPHRPTNVESCPEGKPEALWVEERFTAHIARVR 840 161P2F10Bv.1: 841 DVELLTGLDFYQDKVQPVSEILQLKTYLPTFETTI 875 DVELLTGLDFYQDKVQPVSEILQLKTYLPTFETTI 161P2F10Bv.6: 841 DVELLTGLDFYQDKVQPVSEILQLKTYLPTFETTI 875

TABLE LV Nucleotide sequence of transcript variant 161P2P10B v.7 (SEQ ID NO: 97) ctactttatt ctgataaaac aggtctatgc agctaccagg acaatggaat ctacgttgac 60 tttagcaacg gaacaacctg ttaagaagaa cactcttaag aaatataaaa tagcttgcat 120 tacagggtct ctctcctttg ggatctcacc tcaccacaac ctctgtttcc caggctcaag 180 tgatcctcct gcctcagcct cctgagtagc ttggaccaca ggcacatgcc acaaggctca 240 gctaagtttt tgttcttctt gctttgctgg tgatcatgtc acttggatta ggcctggggc 300 ttggactcag gaaactggaa aagcaaggca gctgcaggaa gaagtgcttt gatgcatcat 360 ttagaggact ggagaactgc cggtgtgatg tggcatgtaa agaccgaggt gattgctgct 420 gggattttga agacacctgt gtggaatcaa ctcgaatatg gatgtgcaat aaatttcgtt 480 gtggagagac cagattagag gccagccttt gctcttgttc agatgactgt ttgcagaaga 540 aagattgctg tgctgactat aagagtgttt gccaaggaga aacctcatgg ctggaagaaa 600 actgtgacac agcccagcag tctcagtgcc cagaagggtt tgacctgcca ccagttatct 660 tgttttctat ggatggattt agagctgaat atttatacac atgggatact ttaatgccaa 720 atatcaataa actgaaaaca tgtggaattc attcaaaata catgagagct atgtatccta 780 ccaaaacctt cccaaatcat tacaccattg tcacgggctt gtatccagag tcacatggca 840 tcattgacaa taatatgtat gatgtaaatc tcaacaagaa tttttcactt tcttcaaagg 900 aacaaaataa tccagcctgg tggcatgggc aaccaatgtg gctgacagca atgtatcaag 960 gtttaaaagc cgctacctac ttttggcccg gatcagaagt ggctataaat ggctcctttc 1020 cttccatata catgccttac aacggaagtg tcccatttga agagaggatt tctacactgt 1080 taaaatggct ggacctgccc aaagctgaaa gacccaggtt ttataccatg tattttgaag 1140 aacctgattc ctctggacat gcaggtggac cagtcagtgc cagagtaatt aaagccttac 1200 aggtagtaga tcatgctttt gggatgttga tggaaggcct gaagcagcgg aatttgcaca 1260 actgtgtcaa tatcatcctt ctggctgacc atggaatgga ccagacttat tgtaacaaga 1320 tggaatacat gactgattat tttcccagaa taaacttctt ctacatgtac gaagggcctg 1380 ccccccgcat ccgagctcat aatatacctc atgacttttt tagttttaat tctgaggaaa 1440 ttgttagaaa cctcagttgc cgaaaacctg atcagcattt caagccctat ttgactcctg 1500 atttgccaaa gcgactgcac tatgccaaga acgtcagaat cgacaaagtt catctctttg 1560 tggatcaaca gtggctggct gttaggagta aatcaaatac aaattgtgga ggaggcaacc 1620 atggttataa caatgagttt aggagcatgg aggctatctt tctggcacat ggacccagtt 1680 ttaaagagaa gactgaagtt gaaccatttg aaaatattga agtctataac ctaatgtgtg 1740 atcttctacg cattcaacca gcaccaaaca atggaaccca tggtagttta aaccatcttc 1800 tgaaggtgcc tttttatgag ccatcccatg cagaggaggt gtcaaagttt tctgtttgtg 1860 gctttgctaa tccattgccc acagagtctc ttgactgttt ctgccctcac ctacaaaata 1920 gtactcagct ggaacaagtg aatcagatgc taaatctcac ccaagaagaa ataacagcaa 1980 cagtgaaagt aaatttgcca tttgggaggc ctagggtact gcagaagaac gtggaccact 2040 gtctccttta ccacagggaa tatgtcagtg gatttggaaa agctatgagg atgcccatgt 2100 ggagttcata cacagtcccc cagttgggag acacatcgcc tctgcctccc actgtcccag 2160 actgtctgcg ggctgatgtc agggttcctc cttctgagag ccaaaaatgt tccttctatt 2220 tagcagacaa gaatatcacc cacggcttcc tctatcctcc tgccagcaat agaacatcag 2280 atagccaata tgatgcttta attactagca atttggtacc tatgtatgaa gaattcagaa 2340 aaatgtggga ctacttccac agtgttcttc ttataaaaca tgccacagaa agaaatggag 2400 taaatgtggt tagtggacca atatttgatt ataattatga tggccatttt gatgctccag 2460 atgaaattac caaacattta gccaacactg atgttcccat cccaacacac tactttgtgg 2520 tgctgaccag ttgtaaaaac aagagccaca caccggaaaa ctgccctggg tggctggatg 2580 tcctaccctt tatcatccct caccgaccta ccaacgtgga gagctgtcct gaaggtaaac 2640 cagaagctct ttgggttgaa gaaagattta cagctcacat tgcccgggtc cgtgatgtag 2700 aacttctcac tgggcttgac ttctatcagg ataaagtgca gcctgtctct gaaattttgc 2760 aactaaagac atatttacca acatttgaaa ccactattta acttaataat gtctacttaa 2820 tatataattt actgtataaa gtaattttgg caaaatataa gtgatttttt ctggagaatt 2880 gtaaaataaa gttttctatt tttccttaaa aaaaaaacgg gaattccggg cttgggaggc 2940 tgaggcagga gactcgcttg aacccgggag gcagaggttg cagtgagcca agattgcgcc 3000 attgcactcc agagcctggg tgacagagca agactacatc tcaaaaaata aataaataaa 3060 ataaaagtaa caataaaaat aaaaagaaca gcagagagaa tgagcaagga gaaatgtcac 3120 aaactattgc aaaatactgt tacactgggt tggctctcca agaagatact ggaatctctt 3180 cagccatttg cttttcagaa gtagaaacca gcaaaccacc tctaagcgga gaacatacga 3240 ttctttatta agtagctctg gggaaggaaa gaataaaagt tgatagctcc ctgattggga 3300 aaaaatgcac aattaataaa gaatgaagat gaaagaaagc atgcttatgt tgtaacacaa 3360 aaaaaattca caaacgttgg tggaaggaaa acagtataga aaacattact ttaactaaaa 3420 gctggaaaaa ttttcagttg ggatgcgact gacaaaaaga acgggatttc caggcataaa 3480 gttggcgtga gctacagagg gcaccatgtg gctcagtgga agacccttca agattcaaag 3540 ttccatttga cagagcaaag gcacttcgca aggagaaggg tttaaattat gggtccaaaa 3600 gccaagtggt aaagcgagca atttgcagca taactgcttc tcctagacag ggctgagtgg 3660 gcaaaatacg acagtacaca cagtgactat tagccactgc cagaaacagg ctgaacagcc 3720 ctgggagaca agggaaggca ggtggtggga gttgttcatg gagagaaagg agagttttag 3780 aaccagcaca tccactggag atgctgggcc accagacccc tcccagtcaa taaagtctgg 3840 tgcctcattt gatctcagcc tcatcatgac cctggagaga ccctgatacc atctgccagt 3900 ccccgacagc ttaggcactc cttgccatca acctgacccc ccgagtggtt ctccaggctc 3960 cctgccccac ccattcaggc cggaattc 3988

TABLE LVI Nucleotide sequence alignment of 161P2F10B v.1 (SEQ ID NO: 98) and 161P2F10B v.7 (SEQ ID NO: 99) Score = 233 bits (121), Expect = 2e-57Identities = 121/121 (100%) Strand = Plus/Plus

Score = 7189 bits (3739), Expect = 0.0Identities = 3739/3739 (100%) Strand = Plus/Plus

TABLE LVII Peptide sequences of protein coded by 161P2F10B v.7 (SEQ ID NO: 100) MSLGLGLGLG LRKLEKQGSC RKKCFDASFR GLENCRCDVA CKDRGDCCWD FEDTCVESTR 60 IWMCNKFRCG ETRLEASLCS CSDDCLQRKD CCADYKSVCQ GETSWLEENC DTAQQSQCPE 120 GFDLPPVILF SMDGFRAEYL YTWDTLMPNI NKLKTCGIHS KYMRAMYPTK TFPNHYTIVT 180 GLYPESHGII DNNMYDVNLN KNFSLSSKEQ NNPAWWHGQP MWLTAMYQGL KAATYFWPGS 240 EVAINGSFPS IYMPYNGSVP FEERISTLLK WLDLPKAERP RFYTMFFEEP DSSGHAGGPV 300 SARVIKALQV VDHAFGMLME GLKQRNLHNC VNIILLADHG MDQTYCNKME YMTDYFPRIN 360 FFYMYEGPAP RVRAHNIPHD FFSFNSEEIV RNLSCRKPDQ HFKPYLTPDL PKRLHYAKNV 420 RIDKVHLFVD QQWLAVRSKS NTNCGGGNHG YNNEFRSMEA IFLAHGPSFK EKTEVEPFEN 480 IEVYNLMCDL LRIQPAPNNG THGSLNHLLK VPFYEPSHAE EVSKFSVCGF ANPLPTESLD 540 CFCPHLQNST QLEQVNQMLN LTQEEITATV KVNLPFGRPR VLQKNVDHCL LYHREYVSGF 600 GKAMRMPMWS SYTVPQLGDT SPLPPTVPDC LRADVRVPPS ESQKCSFYLA DKNITHGFLY 660 PPASNRTSDS QYDALITSNL VPMYEEFRKM WDYFHSVLLI KHATERNGVN VVSGPIFDYN 720 YDGHFDAPDE ITKHLANTDV PIPTHYFVVL TSCKNKSHTP ENCPGWLDVL PFIIPHRPTN 780 VESCPEGKPE ALWVEERFTA HIARVRDVEL LTGLDFYQDK VQPVSEILQL KTYLPTFETT 840 I 841

TABLE LVIII Amino acid sequence alignment of 161P2F10Bv.1. v.1 (SEQ ID NO: 101) and 161P2F10B v.7 (SEQ ID NO: 102) Score = 1789 bits (4634),    Expect = 0.0    Identities = 838/841 (99%), Positives = 841/841 (99%) 161P2F10Bv.1: 35 MSLGLGLGLGLRKLEKQGSCRKKCFDASFRGLENCRCDVACKDRGDCCWDFEDTCVESTR 94 MSLGLGLGLGLRKLEKQGSCRKKCFDASFRGLENCRCDVACKDRGDCCWDFEDTCVESTR 161P2F10Bv.7: 1 MSLGLGLGLGLRKLEKQGSCRKKCFDASFRGLENCRCDVACKDRGDCCWDFEDTCVESTR 60 161P2F10Bv.1: 95 IWMCNKFRCGETRLEASLCSCSDDCLQKKDCCADYKSVCQGETSWLEENCDTAQQSQCPE 154 IWMCNKFRCGETRLEASLCSCSDDCLQKKDCCADYKSVCQGETSWLEENCDTAQQSQCPE 161P2F10Bv.7: 61 IWMCNKFRCGETRLEASLCSCSDDCLQKKDCCADYKSVCQGETSWLEENCDTAQQSQCPE 120 161P2F10Bv.1: 155 GFDLPPVILFSMDGFRAEYLYTWDTLMPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVT 214 GFDLPPVILFSMDGFRAEYLYTWDTLMPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVT 161P2F10Bv.7: 121 GFDLPPVILFSMDGFRAEYLYTWDTLMPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVT 180 161P2F10Bv.1: 215 GLYPESHGIIDNNMYDVNLNKNFSLSSKEQNNPAWWHGQPMWLTAMYQGLKAATYFWPGS 274 GLYPESHGIIDNNMYDVNLNKNFSLSSKEQNNPAWWHGQPMWLTAMYQGLKAATYFWPGS 161P2F10Bv.7: 181 GLYPESHGIIDNNMYDVNLNKNFSLSSKEQNNPAWWHGQPMWLTAMYQGLKAATYFWPGS 240 161P2F10Bv.1: 275 EVAINGSFPSIYMPYNGSVPFEERISTLLKWLDLPKAERPRFYTMYFEEPDSSGHAGGPV 334 EVAINGSFPSIYMPYNGSVPFEERISTLLKWLDLPKAERPRFYTMYFEEPDSSGHAGGPV 161P2F10Bv.7: 241 EVAINGSFPSIYMPYNGSVPFEERISTLLKWLDLPKAERPRFYTMYFEEPDSSGHAGGPV 300 161P2F10Bv.1: 335 SARVIKALQVVDHAFGMLMEGLKQRNLHNCVNIILLADHGMDQTYCNKMEYMTDYFPRIN 394 SARVIKALQVVDHAFGMLMEGLKQRNLHNCVNIILLADHGMDQTYCNKMEYMTDYFPRIN 161P2F10Bv.7: 301 SARVIKALQVVDHAFGMLMEGLKQRNLHNCVNIILLADHGMDQTYCNKMEYMTDYFPRIN 360 161P2F10Bv.1: 395 FFYMYEGPAPRIRAHNIPHDFFSFNSEEIVRNLSCRKPDQHFKPYLTPDLPKRLHYAKNV 454 FFYMYEGPAPRIRAHNIPHDFFSFNSEEIVRNLSCRKPDQHFKPYLTPDLPKRLHYAKNV 161P2F10Bv.7: 361 FFYMYEGPAPRIRAHNIPHDFFSFNSEEIVRNLSCRKPDQHFKPYLTPDLPKRLHYAKNV 420 161P2F10Bv.1: 455 RIDKVHLFVDQQWLAVRSKSNTNCGGGNHGYNNEFRSMEAIFLAHGPSFKEKTEVEPFEN 514 RIDKVHLFVDQQWLAVRSKSNTNCGGGNHGYNNEFRSMEAIFLAHGPSFKEKTEVEPFEN 161P2F10Bv.7: 421 RIDKVHLFVDQQWLAVRSKSNTNCGGGNHGYNNEFRSMEAIFLAHGPSFKEKTEVEPFEN 480 161P2F10Bv.1: 515 IEVYNLMCDLLRIQPAPNNGTHGSLNHLLFVPFYEPSHAEEVSKFSVCGFANPLPTESLD 574 IEVYNLMCDLLRIQPAPNNGTHGSLNHLLFVPFYEPSHAEEVSKFSVCGFANPLPTESLD 161P2F10Bv.7: 481 IEVYNLMCDLLRIQPAPNNGTHGSLNHLLFVPFYEPSHAEEVSKFSVCGFANPLPTESLD 540 161P2F10Bv.1: 575 CFCPHLQNSTQLEQVNQMLNLTQEEITATVKVNLPFGRPRVLQKNVDHCLLYHREYVSGF 634 CFCPHLQNSTQLEQVNQMLNLTQEEITATVKVNLPFGRPRVLQKNVDHCLLYHREYVSGF 161P2F10Bv.7: 541 CFCPHLQNSTQLEQVNQMLNLTQEEITATVKVNLPFGRPRVLQKNVDHCLLYHREYVSGF 600 161P2F10Bv.1: 635 GKAMRMPMWSSYTVPQLGDTSPLPPTVPDCLRADVRVPPSESQKCSFYLADKNITHGFLY 694 GKAMRMPMWSSYTVPQLGDTSPLPPTVPDCLRADVRVPPSESQKCSFYLADKNITHGFLY 161P2F10Bv.7: 601 GKAMRMPMWSSYTVPQLGDTSPLPPTVPDCLRADVRVPPSESQKCSFYLADKNITHGFLY 660 161P2F10Bv.1: 695 PPASNRTSDSQYDALITSNLVPMYEEFRKMWDYFHSVLLIKHATERNGVNVVSGPIFDYN 754 PPASNRTSDSQYDALITSNLVPMYEEFRKMWDYFHSVLLIKHATERNGVNVVSGPIFDYN 161P2F10Bv.7: 661 PPASNRTSDSQYDALITSNLVPMYEEFRKMWDYFHSVLLIKHATERNGVNVVSGPIFDYN 720 161P2F10Bv.1: 755 YDGHFDAPDEITKHLANTDVPIPTHYFVVLTSCKNKSHTPENCPGWLDVLPFIIPHRPTN 814 YDGHFDAPDEITKHLANTDVPIPTHYFVVLTSCKNKSHTPENCPGWLDVLPFIIPHRPTN 161P2F10Bv.7: 721 YDGHFDAPDEITKHLANTDVPIPTHYFVVLTSCKNKSHTPENCPGWLDVLPFIIPHRPTN 780 161P2F10Bv.1: 815 VESCPEGKPEALWVEERFTAHIARVRDVELLTGLDFYQDKVQPVSEILQLKTYLPTFETT 874 VESCPEGKPEALWVEERFTAHIARVRDVELLTGLDFYQDKVQPVSEILQLKTYLPTFETT 161P2F10Bv.7: 781 VESCPEGKPEALWVEERFTAHIARVRDVELLTGLDFYQDKVQPVSEILQLKTYLPTFETT 840 161P2F10Bv.1: 875 I 875 I 161P2F10Bv.7: 841 I 841

TABLE LIX 161P2F10B Expression in Kidney Cancer Clear cell Papillary Chromophobe Transitional Oncocytoma RNA analysis: 33/34 16/19 2/3 (67%) 3/7 (42%) 0/3 (0%) (97%) (84%) Protein analysis: 12/12 5/5 1/3 (33%) 0/3 (0%) 0/2 (0%) (100%) (100%)

TABLE LX 161P2F10B protein expression in normal tissues TISSUE FREQUENCY Kidney 5/5 Prostate 4/8 Bladder 1/4* Colon 2/5* Lung 1/4* Brain 0/1 Breast 0/2 Heart 0/1 Liver 0/3 Ovary 0/1 Pancreas 0/2 Placenta 0/1 Skin 0/1 Spleen 0/1 Testis 0/4 Thymus 0/1 Uterus 0/1 

1. A method of inhibiting the growth of a cancer cell that expresses the protein of SEQ ID NO: 3, the method comprising: administering to the cancer cell a composition whereby the growth of the cancer cell is inhibited, wherein the composition comprises an antibody or antigen binding fragment thereof that specifically binds to the protein, and wherein the antibody or the antigen binding fragment thereof is conjugated to an agent selected from the group consisting of a radioactive isotope, a chemotherapeutic agent and a toxin.
 2. The method of claim 1, wherein the cancer cell is a cell from a tissue selected from the group consisting of kidney, pancreatic, prostate, colon, lung, breast, and ovarian.
 3. The method of claim 1, wherein the antibody is a monoclonal antibody or an antigen binding fragment thereof.
 4. The method of claim 3, wherein the antigen binding fragment is an Fab, F(ab′)2, Fv or sFv fragment.
 5. The method of claim 1, wherein the radioactive isotope is selected from the group consisting of ²¹¹At, ¹³¹I, ¹²⁵I, ⁹⁰Y, ¹⁸⁶Re, ¹⁸⁸Re, ¹⁵³Sm, ²¹²Bi, ³²P and radioactive isotopes of Lu.
 6. The method of claim 1, wherein the chemotherapeutic agent is selected from the group consisting of taxol, actinomycin, mitomycin, etoposide, tenoposide, vincristine, vinbiastine, colchicine, gelonin, and calicheamicin.
 7. The method of claim 1, wherein the toxin is selected from the group consisting of diphtheria toxin, enomycin, phenomycin, Pseudomonas exotoxin (PE) A, PE40, abrin, abrin A chain, mitogellin, modeccin A chain, and alpha-sarcin.
 8. The method of claim 3, wherein the monoclonal antibody is secreted by the hybridoma entitled X41(3)15 (Patent Deposit Designation No. PTA-4791).
 9. The method of claim 3, wherein the monoclonal antibody is secreted by the hybridoma entitled X41(3)37 (Patent Deposit Designation No. PTA-4791).
 10. The method of claim 3, wherein the monoclonal antibody is secreted by the hybridoma entitled X41(4)6 (Patent Deposit Designation No. PTA-4794).
 11. The method of claim 3, wherein the monoclonal antibody is secreted by the hybridoma entitled X41(3)17 (Patent Deposit Designation No. PTA-4792).
 12. The method of claim 3, wherein the monoclonal antibody is secreted by the hybridoma entitled X41(3)50 (Patent Deposit Designation No. PTA-4793).
 13. The method of claim 3, wherein the monoclonal antibody is secreted by the hybridoma entitled X41(3)29 (Patent Deposit Designation No. PTA-4791). 